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## jmol-users

 [Jmol-users] (no subject) From: Patrick J. Carroll - 2001-11-29 20:18:18 I recently "found" Jmol (it's very cool). I'm most interested in using Jmol-Applet on my website to display PDB files, but have found an apparent bug in the PDB reader: if the chemical element being read has two letters in its symbol (Like bromine, Br) the reader only reads the first letter and, e.g., interprets Br as B (boron) and thus does not have the correct atomic radius. Has anyone else seen this problem? 
 [Jmol-users] (no subject) From: Michael T Howard - 2002-09-09 20:04:06 I submitted a bug earlier today (see below). But since there didn't seem to be a lot of activity there I decided to go ahead send it to this mailing list as well. When I compile the jmol source the guide does not get generated. Actually, it *does* get generated, but it comes out on the screen. I think this is an issue with saxon & chunk.xsl. Anyone have any advice? Thanks in advance, Michael ----------- Category: Install Problem Group: None Status: Open Priority: 5 Submitted By: Michael T Howard (michaelthoward) Assigned to: Nobody/Anonymous (nobody) Summary: jmolGuide? + newbie recommendation Initial Comment: I have a number of .mol files which jmol does not recognize. I downloaded the source in order to identify the problem. Recommendation ==== The README.txt file makes no reference to docbook- xsl. As a newbie I was not familiar with this. After some searching I located the docbook (docbook-xsl- 1.54.1) project on sourceforge.net. *I recommend an explicit reference to this project as a system prerequisite in the README.txt file (or somewhere) in the source distribution* Problem ==== I am able to build jmol, but there is a problem with jmolGuide. The jmolGuide target executes and generates several pages of output, followed by the html content of index.html. However, the .html files are not generated into the generatedSource/org/openscience/jmol/Data/guide directory. The jmolHistory target has a similar structure in the build.xml file. This target successfully generates ChangeLog.html into the generatedSource/org/openscience/jmol/Data directory. Thanks in advance, Michael ---------------------------------------------------------------------- >Comment By: Michael T Howard (michaelthoward) Date: 2002-09-09 16:40 Message: Logged In: YES user_id=608250 OK, so (I think) I've figured out that com.icl.saxon.StyleSheet/chunk.xsl are sending all the output to stdout instead of to the appropriate html files ... just don't know why. Q: do I need to fill in some env variables and/or configure in some way? -------------------------------------------------- 
 Re: [Jmol-users] (no subject) From: Michael T Howard - 2002-09-10 11:23:13 Bradley, I successfully built jmol from source using this version of docbook-xsl. Thanks, Michael > New versions of docbook-xsl do not work. This will be investigated. In > the meantime, please use docbook-xsl version 1.40. I have uploaded this > version of docbook-xsl into the files section of the Jmol project under > Tools/Jmol 3 development. > > Thanks, > Bradley > > > ----- Original Message ----- > From: "Michael T Howard" > To: > Sent: Monday, September 09, 2002 1:03 PM > Subject: [Jmol-users] (no subject) > > >> I submitted a bug earlier today (see below). But since there didn't >> seem to be a lot of activity there I decided to go ahead send it to >> this mailing list as well. >> When I compile the jmol source the guide does not get generated. >> Actually, it *does* get generated, but it comes out on the screen. I >> think this is an issue with saxon & chunk.xsl. >> Anyone have any advice? >> >> Thanks in advance, >> Michael >> >> ----------- >> Category: Install Problem >> Group: None >> Status: Open >> Priority: 5 >> Submitted By: Michael T Howard (michaelthoward) >> Assigned to: Nobody/Anonymous (nobody) >> Summary: jmolGuide? + newbie recommendation >> >> Initial Comment: >> I have a number of .mol files which jmol does not >> recognize. >> I downloaded the source in order to identify the >> problem. >> >> Recommendation >> ==== >> The README.txt file makes no reference to docbook- >> xsl. As a newbie I was not familiar with this. After >> some searching I located the docbook (docbook-xsl- >> 1.54.1) project on sourceforge.net. >> *I recommend an explicit reference to this project as >> a system prerequisite in the README.txt file (or >> somewhere) in the source distribution* >> >> Problem >> ==== >> I am able to build jmol, but there is a problem with >> jmolGuide. >> >> The jmolGuide target executes and generates several >> pages of output, followed by the html content of >> index.html. However, the .html files are not generated >> into the >> generatedSource/org/openscience/jmol/Data/guide >> directory. >> >> The jmolHistory target has a similar structure in the >> build.xml file. This target successfully generates >> ChangeLog.html into the >> generatedSource/org/openscience/jmol/Data >> directory. >> >> Thanks in advance, >> Michael >> >> ---------------------------------------------------------------------- >> >> >Comment By: Michael T Howard (michaelthoward) >> Date: 2002-09-09 16:40 >> >> Message: >> Logged In: YES >> user_id=608250 >> >> OK, so (I think) I've figured out that >> com.icl.saxon.StyleSheet/chunk.xsl are sending all the >> output to stdout instead of to the appropriate html files ... >> just don't know why. >> Q: do I need to fill in some env variables and/or configure in >> some way? >> >> -------------------------------------------------- >> >> >> >> >> ------------------------------------------------------- >> This sf.net email is sponsored by: OSDN - Tired of that same old cell >> phone? Get a new here for FREE! >> https://www.inphonic.com/r.asp?r=sourceforge1&refcode1=vs3390 >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users -------------------------------------------------- Miguel Howard miguel@... c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 271 082 12:00 noon Eastern US = cell 011 34 650 525 458 6:00 pm Spain -------------------------------------------------- 
 [Jmol-users] (no subject) From: - 2003-10-10 15:55:04 Hi, I was using Jmol in a web page and recommended it to a colleague as an alternative to accelrys ds/weblab viewer or chime as a tool to communicate the results of docking calculations to synthetic chemists. He had these questions: Does Jmol use proper 3D graphics? The last time I saw it, it looked like Xmol - good for publications but bad when you want to impress the chemists. It would require several extensions: mixed rendering, hiding and showing molecules or parts of molecules, adding lines to indicate e.g. hydrogen bonds, and of course surfaces. Could anyone answer/address those please? I thought I saw something about upcoming 3D graphics. I am not aware of the other features, but thought maybe someone on the list would be. thanks, chris harwell 
 Re: [Jmol-users] (no subject) From: Miguel Howard - 2003-10-10 16:34:01 Chris, > I was using Jmol in a web page and recommended it to a colleague as an > alternative to accelrys ds/weblab viewer or chime as a tool to > communicate the results of docking calculations to synthetic chemists. Good. > He had these questions: > > Does Jmol use proper 3D graphics? The current *development* version *does* have a 3D rendering engine. I recently posted some simple demo pages on the web, but they demonstrate some of the capabilities: http://jmol.sf.net/demo/atoms http://jmol.sf.net/demo/bonds http://jmol.sf.net/demo/trace For something a little more complicated take a look at the following. It is a small application that was auto-converted from chime using the chime2jmol.pl perl script (which is available in cvs, but is not yet generally released). http://jmol.sf.net/bwhite > The last time I saw it, it looked like > Xmol - good for publications but bad when you want to impress the > chemists. I think (hope) that this will do a better job of impressing the chemists ;-) > It would require several extensions: > mixed rendering, I don't know what you mean by 'mixed rendering' > hiding and showing molecules or parts of molecules, The development version of Jmol currently has almost all the capabilities of the RasMol/Chime scripting language. You can select specific atoms and change change colors & size, etc. > adding lines to indicate e.g. hydrogen bonds, In what context do you need to 'add' hydrogen bonds? The RasMol commands for 'monitor' are available and can be used to connect atoms. If other mechanisms are needed, and they seem to be general purpose, then I am sure we can fit them it. > and of course surfaces. of course *surfaces* is the thing that we do *not* yet have :-) We have dotted vanderWaals surfaces and dotted Connolly Solvent Accessible Surfaces, but no true isosurfaces yet. > Could anyone answer/address those please? I thought I saw something > about upcoming 3D graphics. Yep, well they are still upcoming. But take a look at the prerelease demos mentioned above and let us know what you think. Miguel 
 [Jmol-users] perl on Mac OS X From: Miguel - 2003-10-21 13:52:11 >>I assume that you are trying to run on OSX. Please confirm. > > yes, V 5.6 Henry, I have spent several hours over the last two days investigating the situation surrounding perl on OS X. I have found some complicated methods, but nothing straightforward. Therefore, for the time being we are going to wait and see what they included in Panther. Miguel 
 [Jmol-users] (no subject) From: Sriram Ramarathnam - 2004-08-30 14:53:14 hi, Recently i came across this group, i need some help with jmol. I have a pdb file ,i want it to rotate on it's own , just like it does on the link below. http://www.saintmarys.edu/~pbays/Stereochemistry/Fischer.htm and be able to manipulate it .How do i do it??. I don't want to do it on server , i want to do it on a standalone system. looking forward to your reply Thanks Sriram 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2004-08-30 15:20:49 Sriram, take a look at the source code of that page. There you will see that the Jmol applet tag includes It is the "spin on" part that does the rotation. Bob Hanson Sriram Ramarathnam wrote: > hi, > Recently i came across this group, i need some help with jmol. > I have a pdb file ,i want it to rotate on it's own , just like it does on > the link below. > > http://www.saintmarys.edu/~pbays/Stereochemistry/Fischer.htm > > and be able to manipulate it .How do i do it??. I don't want to do it on > server , i want to do it on a standalone system. > > looking forward to your reply > > Thanks > Sriram > > > ------------------------------------------------------- > This SF.Net email is sponsored by BEA Weblogic Workshop > FREE Java Enterprise J2EE developer tools! > Get your free copy of BEA WebLogic Workshop 8.1 today. > http://ads.osdn.com/?ad_id=5047&alloc_id=10808&op=click > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, hansonr@..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:hansonr@... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein 
 Re: [Jmol-users] (no subject) From: Miguel - 2004-08-30 17:18:27 Sriram wrote: > hi, > Recently i came across this group, i need some help with jmol. > I have a pdb file ,i want it to rotate on it's own , just like it does on > the link below. > > http://www.saintmarys.edu/~pbays/Stereochemistry/Fischer.htm > > and be able to manipulate it .How do i do it??. Sriram, I suggest that you look at the demonstration pages at http://www.jmol.org/preview They are simpler pages and should be easier for you to understand. There is other documentation on the jmol web site. > I don't want to do it on > server , i want to do it on a standalone system. If you want to do things 'standalone' then you may want to consider using the Jmol application instead of the JmolApplet. If you definitely want to use the JmolApplet within the context of a web page, then you should put all of your files in the same directory (in order to avoid applet security issues). Miguel 
 [Jmol-users] (no subject) From: Nick Greeves - 2005-04-19 14:06:11 Attachments: Message as HTML > From: Bob Hanson > To: jmol-users@... > Subject: [Jmol-users] power of jmol applet > Reply-To: jmol-users@... > > I'll be interested if the following page works for you: > > http://www.stolaf.edu/people/hansonr/jmol/applet/mscalc/view.htm > > This page demonstrates constructing a JavaScript data structure by > using the "show file" command and then using that information > to do interesting things. Crude, I know. But perhaps it will give > others some ideas. > > I'm interested if using the "show file" command like this at the end > of the loading script works. Mac users? Do you see the contents of the > MOL file listed? Works fine here on Mac OS X. I see the coordinates and can highlight each atom in red (and in the table). The rest of the molecule goes green when clicked. Interesting.... All the best Nick -- WWW Pages: http://www.liv.ac.uk/Chemistry/Staff/greeves.html Tel: +44 (0)151-794-3506 (3500 secretary, 7886 voice mail) 
 [Jmol-users] (no subject) From: J. Dennis Pollack - 2005-08-27 14:58:24 Hi, Is ver 10 of jmol available for WinXP Pro? If so where? If not what ver is? And, where can I dwnld that ver? Thanks, JDPollack 
 Re: [Jmol-users] (no subject) From: Egon Willighagen - 2005-08-29 08:09:48 On Saturday 27 August 2005 04:58 pm, J. Dennis Pollack wrote: > Is ver 10 of jmol available for WinXP Pro? If so where? If not what ver is? > And, where can I dwnld that ver? Jmol is written in Java and can be run on all platforms for which a Java virtual machine is available. A JVM for WinXP (JRE 5.0) can be downloaded from [1], and Jmol itself can be downloaded from [2]. Egon 1. http://java.sun.com/j2se/1.5.0/download.jsp 2. http://jmol.sourceforge.net/download/ 
 [Jmol-users] (no subject) From: Muriel Crouvoisier - 2005-09-14 15:12:29 Hello, I 'm novice. I want to use Jmol to see a protein structure but the PDB file contains two chains. Is it possible to select only one chain? Thanks Muriel Crouvoisier 
 Re: [Jmol-users] (no subject) From: Miguel - 2005-09-22 01:14:51 > Hello, > I 'm novice. I want to use Jmol to see a protein structure but the PDB > file > contains two chains. > Is it possible to select only one chain? In Jmol one selects atoms and they applies properties to the atoms. You need to select the chain that you want to hide and then turn off the atoms and the bonds. select :B; spacefill off; wireframe off; Miguel 
 [Jmol-users] (no subject) From: David Leader - 2005-09-29 09:16:10 Miguel summarized the situation regarding automatic identification of protein secondary structures and jmol and concluded by saying: >My current position is as follows: > >Some else needs to lead the effort to get automatic identification of >protein secondary structures built into Jmol. I believe that this needs to >be someone who understands the problem and has implementation experience. > >I will certainly support the effort in any way that I can, but I will not >lead the effort. This is an eminently reasonable position. I think we should thank Miguel for the time he spent trying to get the relevant people in the protein structure community to co-operate. My personal opinion is that his failure reflects very badly on that community, certain sections of which have a history of selfishness in relation both to structural data and computer algorithms. This is most unfortunate for Jmol as automatic secondary structure prediction is one of the key Rasmol features (according to one of my colleagues) that Jmol lacks. Did anyone ever try to approach Roger Sayle, who presumably wrote devised the algorithm that handles this in Rasmol? David -- _______________________________________________________________ David P.Leader, Biochemistry and Molecular Biology Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader _______________________________________________________________ 
 Re: [Jmol-users] (no subject) From: Miguel - 2005-09-29 12:48:22 David wrote: > My personal opinion is that his failure reflects very > badly on that community, certain sections of which > have a history of selfishness in relation both to > structural data and computer algorithms. Just to clarify (and give people the benefit of the doubt) ... My attempts were made 18 to 20 months ago. At the time Jmol had a much smaller following, and I did not have contacts who could approach these people, explain the situation, and 'make the pitch' on behalf of Jmol. > This is most unfortunate for Jmol as automatic secondary structure > prediction is one of the key Rasmol features (according to one of my > colleagues) that Jmol lacks. Did anyone ever try to approach Roger > Sayle, who presumably wrote devised the algorithm that handles this > in Rasmol? I exchanged a few email messages with Roger Sayle in Dec 2003. The RasMol source code had been released in the public domain up through version 2.6 beta 2 ... but I wanted to get his 'blessing' prior to lookin= g at the source code. A copy of Roger's email response is in the Jmol cvs source code repository. Up to that point I had worked on Jmol independently. However, I felt the need to look at the RasMol source code because I was working on hydrogen bonding ... and I felt like I had reached a dead-end. (The problem is compounded by the fact that the hydrogen atoms are not present in most .pdb files). Looking at the RasMol source code was useful to me. It helped me understand how the 'classical' hydrogen bonds are supposed to work. From that, I was able to build an implementation that was appropriate for the Jmol data structures. I was able to extend it a bit ... and I think that Jmol does a marginally better job than RasMol at hydrogen bond identification in some situations. My attempts at protein secondary structure identification came shortly after this. In this case, I was unable to gain much insight from reading the RasMol source code ... I could not make the connection between the RasMol source and the text description of the algorithms listed in the Kabsch & Sander DSSP paper. After that I went looking for other implementations. At this point I suppose I could take another look at the RasMol source. Frankly, I had completely forgotten about it. But, as I said in my previous message, I believe it would be best if this effort was led by someone with a biochemistry background who has an interest in and understanding of the problem space. Miguel 
 [Jmol-users] (no subject) From: Aaron Glimme - 2005-11-19 07:29:01 I've been using jchempaint for a while to draw structures for my chemistry tests, now I need to turn some of them in to 3d models and I'm having some trouble. I've tried saving the file as a MDL MOL file and CML files and then opening it in Jmol. There are two issues with this that I haven't been able to figure out. The first is the bond length seems really large in Jmol I'm having trouble getting the files to look like a ball and stick model. The second is the geometry isn't working, the models come out in a 2d plane, is there some trick or script I need to run to get the geometry right. I haven't been able to figure it out yet, any help would be much appreciated. I'm using the latest versions of all the apps in Mac OS X 1.4.3. Aaron Glimme Berkeley High School 
 Re: [Jmol-users] (no subject) From: Miguel - 2005-11-19 13:47:06 Aaron wrote: > The first is the bond length seems really large in Jmol I'm having > trouble getting the files to look like a ball and stick model. I may be mistaken, but I believe that jchempaint is saving the atom positions in the incorrect units. I believe that jchempaint stores the atom coordinates in pixels. Jmol (and, I believe, the .mol format) expect the coordinates in angstroms. > The second is the geometry isn't working, the models > come out in a 2d plane, jchempaint is a 2d drawing package. > is there some trick or script I need to run to get the > geometry right. I haven't been able to figure it out > yet, any help would be much appreciated. Calculating 3D molecular structure from a 2D representation is a non-trivial problem. Miguel 
 Re: [Jchempaint-user] Re: [Jmol-users] (no subject) From: Aaron Glimme - 2005-11-19 20:03:38 Thanks all! I thought based on the CDK demo web page that the =20 jchempaint and jmol would talk to each other, but it looks like there =20= is more going on than I thought. I'll look in to the suggestions that =20= I've got. Cheers. Aaron Glimme Berkeley High School On 19-Nov, 2005, at 05:46, Miguel wrote: > Aaron wrote: > >> The first is the bond length seems really large in Jmol I'm having >> trouble getting the files to look like a ball and stick model. > > I may be mistaken, but I believe that jchempaint is saving the atom > positions in the incorrect units. > > I believe that jchempaint stores the atom coordinates in pixels. Jmol > (and, I believe, the .mol format) expect the coordinates in angstroms. > >> The second is the geometry isn't working, the models >> come out in a 2d plane, > > jchempaint is a 2d drawing package. > >> is there some trick or script I need to run to get the >> geometry right. I haven't been able to figure it out >> yet, any help would be much appreciated. > > Calculating 3D molecular structure from a 2D representation is a > non-trivial problem. > > > Miguel > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick > _______________________________________________ > Jchempaint-user mailing list > Jchempaint-user@... > https://lists.sourceforge.net/lists/listinfo/jchempaint-user > 
 [Jmol-users] (no subject) From: jeff gardner - 2006-01-07 01:33:29 Attachments: Message as HTML Hey guys, I'm trying to check out the Jmol project, but I think the sourceforge server is on the fritz: cvs -d:pserver:anonymous@...:/cvsroot/jmol co -d Jmol-HEAD Jmol can't create temporary directory /tmp/cvs-serv30694 No space left on device I've tried several times with the same result.... Join FSF as an Associate Member at: http://member.fsf.org/join?referrer=3479 --------------------------------- Yahoo! Photos Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever.
 Re: [Jmol-users] (no subject) From: Egon Willighagen - 2006-01-07 01:41:55 On Saturday 07 January 2006 02:33, jeff gardner wrote: > Hey guys, I'm trying to check out the Jmol project, but I think the > sourceforge server is on the fritz: > > cvs -d:pserver:anonymous@...:/cvsroot/jmol co -d Jmol-HEAD Jmol > can't create temporary directory /tmp/cvs-serv30694 > No space left on device > > I've tried several times with the same result.... On [1] they mention a hard ware failure... but that was already in Nov 2005... Try again tomorrow. Egon 1.http://sourceforge.net/docman/display_doc.php?docid=2352&group_id=1 -- e.willighagen@... PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen Blog: http://chem-bla-ics.blogspot.com/ http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 
 Re: [Jmol-users] (no subject) From: Miguel - 2006-01-07 01:43:24 > Hey guys, I'm trying to check out the Jmol project, but I think the > sourceforge server is on the fritz: > > cvs -d:pserver:anonymous=40cvs.sf.net:/cvsroot/jmol co -d Jmol-HEAD Jm= ol > can't create temporary directory /tmp/cvs-serv30694 > No space left on device > > I've tried several times with the same result.... Agreed. That is something that sourceforge will have to take care of. Try again tomorrow. Miguel 
 [Jmol-users] (no subject) From: ranjan sharma - 2006-07-07 06:52:20 Attachments: Message as HTML
 [Jmol-users] (no subject) From: Craig T Martin - 2006-09-29 14:47:47 Attachments: Message as HTML Rolf, Great idea, but it didn't work on my Mac w/ Safari (10.4.7, latest =20 everything). I get the following error message saying that Safari =20 needs a plug-in. "The page =93Embedded Image Demo=94 has content of MIME type = =93image/jpg=94. Because you don=92t have a plug-in installed for this MIME type, this =20= content can=92t be displayed." Craig Martin > Message: 8 > Date: Fri, 29 Sep 2006 15:15:16 +0200 > From: Rolf Huehne > Subject: [Jmol-users] Saving image with applet - possible solution > Message-ID: <451D1C64.8090309@...> > > Hi, > > I think I found a solution to save images from the applet without the > need of a server. > The solution is supposed to work at least for most current =20 > non-'Internet > Explorer' browsers. > > The idea is quite simple: > > 1) the javascript Jmol interface requests an image from Jmol > 2) Jmol returns the image data to the interface > 3) the image is inserted as value into the HTML code of the page for a > (predefined?) object > 4) the browser displays the image in the page > 5) the user saves the image using the "Save image..." dialog > > I have set up a little demonstration page that illustrates this =20 > technique: > http://www.fli-leibniz.de/ImgLibPDB/pages/embedded_image_demo.html > ....... > > Regards, > Rolf Craig Martin cmartin@... 
 [Jmol-users] (no subject) From: Frieda Reichsman - 2007-03-01 03:10:05 Attachments: Message as HTML Say I have 3 files loaded but my set of labels should appear on only one of them. I also want to be able to turn on and off the display of the three proteins at will. Is there an easy way to select a series of single atoms for labeling and have the label apply only to one file? Or is the only way to do this to repeat "select file=1 and ..." over and over, like so: select file=1 and 263.n label helix 1 select file=1 and 357.ca label helix 2 etc., etc. In other words is there some way to say, "the following selections apply ONLY to file =1" (and then also end it in some way)? /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2007-03-01 04:48:38 Frieda Reichsman wrote: > Say I have 3 files loaded but my set of labels should appear on only > one of them. I also want to be able to turn on and off the display of > the three proteins at will. > > Is there an easy way to select a series of single atoms for labeling > and have the label apply only to one file? > > Or is the only way to do this to repeat "select file=1 and ..." over > and over, like so: > > select file=1 and 263.n > label helix 1 > If it's one model per file, you can just use the old syntax: select 263.n/1; label helix1 Certainly you need only the number of select/label combinations as you have distinct labels, but other than that, yes, you need to specify the atom and model number to get the label on just that atom. > In other words is there some way to say, "the following selections > apply ONLY to file =1" (and then also end it in some way)? > Well, you could do: select 263.n; label helix1 select 283.n; label helix2 ... select file != 1 labels off That is, just put all the labels in, but then in the end turn the unwanted ones off. Bob > > /////////////////////////////////////////// > > > Frieda Reichsman, PhD > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /////////////////////////////////////////// > > > 
 Re: [Jmol-users] (no subject) From: Harris Procopiou - 2007-03-01 12:15:28 I try to load multiple files but i can't... I 'm working with perl : print "
"; The problem is quotes... how can i do this ? I tried : print "
"; But it does not work too. And : print "
"; The same.. Thanx Bob Hanson a écrit : > Frieda Reichsman wrote: > > >> Say I have 3 files loaded but my set of labels should appear on only >> one of them. I also want to be able to turn on and off the display of >> the three proteins at will. >> >> Is there an easy way to select a series of single atoms for labeling >> and have the label apply only to one file? >> >> Or is the only way to do this to repeat "select file=1 and ..." over >> and over, like so: >> >> select file=1 and 263.n >> label helix 1 >> >> > If it's one model per file, you can just use the old syntax: > > select 263.n/1; label helix1 > > Certainly you need only the number of select/label combinations as you > have distinct labels, but other than that, yes, you need to specify the > atom and model number to get the label on just that atom. > > >> In other words is there some way to say, "the following selections >> apply ONLY to file =1" (and then also end it in some way)? >> >> > Well, you could do: > > select 263.n; label helix1 > select 283.n; label helix2 > ... > select file != 1 > labels off > > That is, just put all the labels in, but then in the end turn the > unwanted ones off. > > Bob > > >> /////////////////////////////////////////// >> >> >> Frieda Reichsman, PhD >> >> Molecules in Motion >> >> Interactive Molecular Structures >> >> http://www.moleculesinmotion.com >> >> >> /////////////////////////////////////////// >> >> >> >> > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > 
 Re: [Jmol-users] (no subject) From: Frieda Reichsman - 2007-03-01 12:50:47 Attachments: Message as HTML Hi Harris, > jmolInitialize("Jmol.js"); is incorrect - in the parenthesis should be the path to the Jmol =20 applet. If the applet is in the same directory, use simple a single =20 dot (.). Jmol.js must be referred to in the header, like this: > "; > > The problem is quotes... how can i do this ? > > I tried : > > print " >
> > "; > > But it does not work too. And : > > print " >
> > "; > > The same.. > > Thanx > > Bob Hanson a =E9crit : >> Frieda Reichsman wrote: >> >> >>> Say I have 3 files loaded but my set of labels should appear on only >>> one of them. I also want to be able to turn on and off the =20 >>> display of >>> the three proteins at will. >>> >>> Is there an easy way to select a series of single atoms for labeling >>> and have the label apply only to one file? >>> >>> Or is the only way to do this to repeat "select file=3D1 and ..." = over >>> and over, like so: >>> >>> select file=3D1 and 263.n >>> label helix 1 >>> >>> >> If it's one model per file, you can just use the old syntax: >> >> select 263.n/1; label helix1 >> >> Certainly you need only the number of select/label combinations as =20= >> you >> have distinct labels, but other than that, yes, you need to =20 >> specify the >> atom and model number to get the label on just that atom. >> >> >>> In other words is there some way to say, "the following selections >>> apply ONLY to file =3D1" (and then also end it in some way)? >>> >>> >> Well, you could do: >> >> select 263.n; label helix1 >> select 283.n; label helix2 >> ... >> select file !=3D 1 >> labels off >> >> That is, just put all the labels in, but then in the end turn the >> unwanted ones off. >> >> Bob >> >> >>> /////////////////////////////////////////// >>> >>> >>> Frieda Reichsman, PhD >>> >>> Molecules in Motion >>> >>> Interactive Molecular Structures >>> >>> http://www.moleculesinmotion.com >>> >>> >>> /////////////////////////////////////////// >>> >>> >>> >>> >> >> >> ---------------------------------------------------------------------=20= >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to =20 >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?=20 >> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// 
 Re: [Jmol-users] (no subject) From: Egon Willighagen - 2007-03-01 13:34:53 Hi Harris, On Thursday 01 March 2007 13:15:16 Harris Procopiou wrote: > I try to load multiple files but i can't... I 'm working with perl : > > print " >
> > "; In Perl you can escape the quotes with \"... so try this: print "
"; Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ 
 Re: [Jmol-users] (no subject) From: Rolf Huehne - 2007-03-01 13:49:44 Harris Procopiou wrote: > I try to load multiple files but i can't... I 'm working with perl : > > print " >
> > "; > > The problem is quotes... how can i do this ? > > I tried : > > print " >
> > "; > > But it does not work too. And : > > print " >
> > "; > > The same.. > > Hi Harris, since you mentioned perl as the script language you are using to create the HTML code I guess your question refers to the syntax errors you will get in perl if you try the above 'print' commands. There are two methods in perl to solve this problem. The first one is to 'escape' the double quotes inside the 'print' statement with a backslash,e.g.: print "jmolApplet(300, \"load 'fileset' '1BZ8.pdb' '1C26.pdb'\");"; The disadvantage of this method is that the text is less good readable and that you have to change the HTML code you might have tested in a plain HTML text before you started to integrate it into your perl script. Therefore I prefer the second method: using the general quoting operator 'qq'. The above example could look like this: print qq{jmolApplet(300, "load 'fileset' '1BZ8.pdb' '1C26.pdb");}; You can replace the brace ('{') behind the 'qq' by any other non-alphanumeric character. Then the end brace ('}') must also be replaced by the same character (or the corresponding closing bracket character if you use '(' or '['). In my work the brace has proven to work in most cases for HTML code. Regards, Rolf 
 Re: [Jmol-users] (no subject) From: Frieda Reichsman - 2007-03-01 12:53:12 Attachments: Message as HTML Thanks, Bob, I never seem to remember the /model syntax, and the last solution is great - so simple. Frieda On Feb 28, 2007, at 11:48 PM, Bob Hanson wrote: > Frieda Reichsman wrote: > >> Say I have 3 files loaded but my set of labels should appear on only >> one of them. I also want to be able to turn on and off the display of >> the three proteins at will. >> >> Is there an easy way to select a series of single atoms for labeling >> and have the label apply only to one file? >> >> Or is the only way to do this to repeat "select file=1 and ..." over >> and over, like so: >> >> select file=1 and 263.n >> label helix 1 >> > If it's one model per file, you can just use the old syntax: > > select 263.n/1; label helix1 > > Certainly you need only the number of select/label combinations as you > have distinct labels, but other than that, yes, you need to specify > the > atom and model number to get the label on just that atom. > >> In other words is there some way to say, "the following selections >> apply ONLY to file =1" (and then also end it in some way)? >> > Well, you could do: > > select 263.n; label helix1 > select 283.n; label helix2 > ... > select file != 1 > labels off > > That is, just put all the labels in, but then in the end turn the > unwanted ones off. > > Bob > >> >> /////////////////////////////////////////// >> >> >> Frieda Reichsman, PhD >> >> Molecules in Motion >> >> Interactive Molecular Structures >> >> http://www.moleculesinmotion.com >> >> >> /////////////////////////////////////////// >> >> >> > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// 
 [Jmol-users] controlling three applets with one set of radio buttons From: John Tweedie - 2007-03-01 23:07:50 Attachments: Message as HTML Hello I have a page with three applets (loaded columns in a table row , B- A- and Z DNA) with a set of radio buttons for each applet in the same table row. I want to have a single set of radio buttons that relate to all three applets at once. I can set up buttons outside the table and get them to apply to the one applet at a time using a "jmolSetTarget" and specifying the applet but cannot get them to work on all 3. Regards John Tweedie Associate Professor in Biochemistry Institute of Molecular BioSciences Massey University Private Bag 11-222 Palmerston North NEW ZEALAND e-mail (Massey): j.tweedie@... Phone (Massey):64 6 350 5515 Ext 2581 e-mail (Home): jtweedie1@... Phone (Home): 64 6 358 0150 Home Address: 15 Annandale Avenue Palmerston North NEW ZEALAND On Mar 1, 2007, at 05:48 PM, Bob Hanson wrote: > Frieda Reichsman wrote: > >> Say I have 3 files loaded but my set of labels should appear on only >> one of them. I also want to be able to turn on and off the display of >> the three proteins at will. >> >> Is there an easy way to select a series of single atoms for labeling >> and have the label apply only to one file? >> >> Or is the only way to do this to repeat "select file=1 and ..." over >> and over, like so: >> >> select file=1 and 263.n >> label helix 1 >> > If it's one model per file, you can just use the old syntax: > > select 263.n/1; label helix1 > > Certainly you need only the number of select/label combinations as you > have distinct labels, but other than that, yes, you need to specify > the > atom and model number to get the label on just that atom. > >> In other words is there some way to say, "the following selections >> apply ONLY to file =1" (and then also end it in some way)? >> > Well, you could do: > > select 263.n; label helix1 > select 283.n; label helix2 > ... > select file != 1 > labels off > > That is, just put all the labels in, but then in the end turn the > unwanted ones off. > > Bob > >> >> /////////////////////////////////////////// >> >> >> Frieda Reichsman, PhD >> >> Molecules in Motion >> >> Interactive Molecular Structures >> >> http://www.moleculesinmotion.com >> >> >> /////////////////////////////////////////// >> >> >> > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > 
 Re: [Jmol-users] (no subject) From: Angel Herraez - 2007-03-01 13:31:07 Hello Harris Yes, it seems a quotes problem. First, try this: Jmol requires double quotes for load, so you should use single quotes for the javascript:
However, since you have a more external set of double quotes for your "print", it may not work. I think I read about the use of ", but right now I canot find it. If I do, I will post again. If you want to try, it could be (I haven't checked):

 Re: [Jmol-users] controlling three applets with one set of radio buttons From: Angel Herraez - 2007-03-01 23:53:36 Hi John How about setting a javascript function that will do the job three times, one for each applet? 
 [Jmol-users] (no subject) From: - 2007-03-01 14:28:46 
thanx all for your help but I tried all the possibilities and it does= not work...

The last method i tried is :

print qq{            = ;            <for= m>
&nbs= p;             = <script>
&= nbsp;           &nbs= p;        jmolInitialize("../softs/= jmol-10.2.0");
&n= bsp;            = ;       jmolApplet(300, "load 'fileset' = '../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;"= ;);
=              &l= t;/script>
&n= bsp;            = ;  </form>
};
Is this command correct ? jmolApplet(300, "load 'fileset' '1B= Z8.pdb' '1C26.pdb'; select */2;");

Should the applet show a= nything or not ?

Thanx

Harris =0D

 Re: [Jmol-users] (no subject) From: Egon Willighagen - 2007-03-01 14:32:16 On Thursday 01 March 2007 15:28:35 harris@... wrote: > The last method i tried is : > > print qq{ > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 jmolInitialize("../softs/jmol-10.2.0"); > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 jmolApplet(300, "load 'fileset' > '../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;"); > > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 > =A0=A0=A0=A0=A0=A0=A0 }; > > Is this command correct ? jmolApplet(300, "load 'fileset' '1BZ8.pdb' > '1C26.pdb'; select */2;"); You still need to apply what Angel mentioned: switch the " and ' in the loa= d=20 command. So: print qq{
}; E. =2D-=20 CUBIC blog: http://chem-bla-ics.blogspot.com/ 
 [Jmol-users] (no subject) From: - 2007-03-01 14:40:44 

ok thank you...

Now when I do :

jmolApplet(300, 'load "fileset" "1BZ8.pdb" &q= uot;1C26.pdb"; select */1;');

It shows 1BZ8 structure. But if i = do :

jmolApplet(300, 'load "fileset" "1BZ8.pdb&q= uot; "1C26.pdb"; select */2;');

It shows nothi= ng.. .is it normal ?

Egon Willighagen a =C3=A9crit&nbs= p;:

=0D
On Thursday 01 March 2007 15:28:35 harris@... wrote:
=0D
The last method i tried is :

print qq{
&= nbsp;           &nbs= p;           <form>=
&nb= sp;            <s= cript>
=             &nb= sp;       jmolInitialize("../softs/jmol-= 10.2.0");
&= nbsp;           &nbs= p;      jmolApplet(300, "load 'fileset'
= '../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;"= ;);
</script>
&nb= sp;            =     </form>
&= nbsp; };

Is this command correct ? jmolApplet(300, "load 'f= ileset' '1BZ8.pdb'
'1C26.pdb'; select */2;");
=0D

You still need to apply what Angel mentioned: switch th= e " and ' in the load
command. So:

print qq{
= <form>
<script&g= t;
jmolInitialize("../softs/jmol-10= .2.0");
"../pdb_structures/1BZ8.pdb" "../pdb_struc= tures/1C26.pdb"; select */1;');
</script>
= </form>
};

E.

= =0D
=0D =0D


 Re: [Jmol-users] (no subject) From: Frieda Reichsman - 2007-03-01 15:44:43 Attachments: Message as HTML you need to insert the command file 0 which makes all the files you loaded "displayable" (but not displayed) so say jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; file 0; select =20= */2; spacefill on;'); the last command is just to actually render the structure in a style, =20= choose whatever rendering you like. Also, the reason that select */1 worked was simply that when you load multiple files, only the first =20 one shows up by default. Frieda On Mar 1, 2007, at 9:40 AM, wrote: > > ok thank you... > > > Now when I do : > > > jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;'); > > It shows 1BZ8 structure. But if i do : > > jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;'); > > > It shows nothing.. .is it normal ? > > > Egon Willighagen a =E9crit : > > On Thursday 01 March 2007 15:28:35 harris@... wrote: > The last method i tried is : > > print qq{ > > > > }; > > Is this command correct ? jmolApplet(300, "load 'fileset' '1BZ8.pdb' > '1C26.pdb'; select */2;"); > > You still need to apply what Angel mentioned: switch the " and ' in =20= > the load > command. So: > > print qq{ > > > > }; > > E. > > > > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV____________________________= ____=20 > _______________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// 
 Re: [Jmol-users] (no subject) From: Frieda Reichsman - 2007-03-01 15:56:31 Attachments: Message as HTML oops - I misspoke -- I said: > > you need to insert the command > file 0 > which makes all the files you loaded "displayable" (but not displayed) > BUT I was incorrect. "file 0" actually does display all the files loaded. So instead say so say: jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; file 0; display file=2;'); the command display file=2 is what displays ONLY file 2. Below is a "reprint" of a complete explanation that Bob H wrote to the list yesterday (in response to my questions). Frieda ------------------------ reprint ------------------------ Bob said: > The logic is supposed to be: > > "display x" hides all atoms except x. > "hide x" displays all atoms except x. > > To this we add: > > display xxx # display ONLY x > hide not xxx # same thing! > > display not xxx # display everything but x > hide xxx # same thing! > > display hidden # toggle shown for unshown > hide displayed # same thing! > > display displayed and not xxx # remove xxx from the display --- what > you want here > hide hidden or xxx # same thing! > > display displayed or xxx # add x to the display --- also what you > want > hide hidden and not xxx # add x to the display > > So just don't use "hide" if it confuses you. It is never necessary. > Thinking in terms of what is displayed gets you anything you want. The > key for this situation is to use "displayed" as part of that > checkbox item. > > [x] file 1: [x]"display displayed or file=1" [ ] "display > displayed > and not file=1" > [x] file 2 : [x]"display displayed or file=2" [ ] "display > displayed > and not file=2" > [x] file 3 : [x]"display displayed or file=3" [ ] "display > displayed > and not file=3" > 
 Re: [Jmol-users] (no subject) From: Angel Herraez - 2007-03-02 13:57:53 Hi Harris Although others had posted more detailed solutions to your question, I think the problem you had with > jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;'); > It shows 1BZ8 structure. But if i do : > > > jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;'); > It shows nothing.. .is it normal ? is that, when several files are loaded, they are assigned frame/model numbers 1001, 2001, not 1, 2. So, in your examples: jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1001;'); # first model in 1BZ8.pdb jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2001;'); # first model in 1C26.pdb The new syntax in Jmol 11.1.x allows to use the more clear "file 1", "file 2" and "1.1", "1.2", "2.1" identifiers, which have already been recommended by others. HTH 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2007-03-02 22:47:19 In 11.1.x we are recommending going to a simpler method of naming models in multiple file mode: Files have each one model: 1.1, 2.1, 3.1, .... Files have more than one model: 1.1, 1.2, 1.3, ... 2.1, 2.2, 2.3.... etc. Then, in analogy to model 0 for displaying all models, now we have: model 1.0 # all models in File 1 The original idea of 1001 2001 3001 still is implemented, but this is better. Also, in 11.1.x I fixed it so that model 1 model 2 etc. works as well, as long as the files really only have one model each. That's because "model 1" is the same as "model 1.0" -- "all models in file 1". So if you say model 1 or model 1.0 that's the same -- all models in file 1. I think this works reasonably intuitively. Bob Bob Angel Herraez wrote: >Hi Harris > >Although others had posted more detailed solutions to your question, >I think the problem you had with > > > >>jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;'); >>It shows 1BZ8 structure. But if i do : >> >> >>jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;'); >>It shows nothing.. .is it normal ? >> >> > > >is that, when several files are loaded, they are assigned frame/model >numbers 1001, 2001, not 1, 2. So, in your examples: >jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select >*/1001;'); # first model in 1BZ8.pdb >jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select >*/2001;'); # first model in 1C26.pdb > >The new syntax in Jmol 11.1.x allows to use the more clear "file 1", >"file 2" and "1.1", "1.2", "2.1" identifiers, which have already >been recommended by others. > >HTH > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys-and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > 
 [Jmol-users] (no subject) From: Craig T Martin - 2007-05-03 12:49:53 Attachments: Message as HTML > Message: 3 > Date: Wed, 02 May 2007 19:14:11 -0500 > From: Bob Hanson > Subject: [Jmol-users] signed applets > To: jmol-users@... > Message-ID: <46392953.9090809@...> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I looking for someone who is using the signed applet. Dear Bob, I use it all the time, though only for local file access, not from one server to another. In my usage, i have a javascript that figures out if the access is local or to a server. If the former, then it uses the signed applet. Thus all of my local development is with the signed applet. However, I've had a hard time keeping up with the (fantastic) pace of your development. The most recent version I've used is 10.9.98. The signed applet works great with that (on a Mac, usually Safari). Did you have a specific question? Craig Craig Martin cmartin@... 
 Re: [Jmol-users] (no subject) From: Craig T Martin - 2007-05-03 17:28:38 Attachments: Message as HTML Bob, As someone else pointed out, i think, when you access the signed applet, it will ask you for permission to run. A dialog will pop up before Jmol fully loads. If you get that dialog, and then everything after that goes smoothly, then the signed applet is working. It will only ask you once per session. To see the request again, you'll have to quit your browser and then reopen. You can pull down a test that when run locally should automatically run the trusted applet at: ; Craig Craig Martin cmartin@... On May 3, 2007, at 11:31 AM, Bob Hanson wrote: > Craig T Martin wrote: > >>> Message: 3 >>> Date: Wed, 02 May 2007 19:14:11 -0500 >>> From: Bob Hanson > >>> Subject: [Jmol-users] signed applets >>> To: jmol-users@... >> users@...> >>> Message-ID: <46392953.9090809@... >> 46392953.9090809@...>> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> I looking for someone who is using the signed applet. >> >> >> Dear Bob, >> >> I use it all the time, though only for local file access, not >> from one server to another. >> >> In my usage, i have a javascript that figures out if the access >> is local or to a server. If the former, then it uses the signed >> applet. Thus all of my local development is with the signed applet. >> >> However, I've had a hard time keeping up with the (fantastic) >> pace of your development. The most recent version I've used is >> 10.9.98. The signed applet works great with that (on a Mac, >> usually Safari). >> >> Did you have a specific question? >> > Yes. What should I do to test that I have the signed applet working? > >> Craig >> >> Craig Martin >> cmartin@... >> >> >> > 
 [Jmol-users] Jmol 11.1.30 From: Bob Hanson - 2007-05-03 21:06:57 Jmol 11.1.30 is ready for release, Nico. Signed applet tests successful and, for example, loads files directly from RCSB's depository simply with load =xxxx where =xxxx is an equal sign followed by a four-digit ID. I recommend that if you want to use the signed applet you use the single-file format of initialization: jmolInitialize(".", "JmolAppletSigned.jar") rather than jmolInitialize(".", true) becaue "true" gives you a download of all the separate jar files, starting with JmolAppletSigned0.jar, and at least Opera asks for an OK on the certificate for every one of them individually. That's a bit of a pain. OK, features. Not too many: full support for switching languages, including a new "language" menu item --------------------------------------------------------------------------- Now you can switch languages anytime you want. Just pop up the menu and select the new "language" item near the bottom. WE NEED PEOPLE TO VOLUNTEER TO DO MORE TRANSLATIONS, even in just the set of languages we are supporting. It would be nice just to get that menu put translation done. Someone want to work on this? # # Jmol.js: # # jmolSetCallback("language", "de") # # Jmol scripting: # # language = "de" # # Menu: # # new language submenu with checkboxes. # # allows for efficient specific file reader options for the applet (particularly) # _spinning variable ------------------ You can now check in IF commands for whether spinning is on or off and script accordingly. For example: wasSpinning = _spinning load myfile.pdb if(wasSpinning);spin on;endif better handling of spin in relation to zoomTo and moveTo -------------------------------------------------------- If the model is spinning when a zoomTo or moveTo command is executed, or if the user uses the mouse to rotate the model, then spinning is halted and only resumes one full second after the manipulation is complete. zoomTo and moveTo the same location changed to no time delay -------------------------------------------------------------------------------- Previously if you did two of the same zoomTo or moveTo operations in a row, Jmol would appear to stall while just counting seconds. That is no longer the case. The second zoomTo or moveTo is simply skipped. hover now is turned off during spinning or user manipulation of the model -------------------------------------------------------------------------- I noticed that hover was picking up atom labels under the mouse when the model was rotating by and considered that a bug. Now when the model is spinning, moving the mouse over atoms (or moving atoms under the mouse) does not show the hover tag. If spinning is stopped, the hover action returns. Pqr reader ---------- Jmol now reads Pqr data files created using PDB2PQR file type forcing ----------------- This feature is of no current use; Jmol correctly assigns file type based on file contents to all file types it reads. But in the future two "flavors" of a format may be difficult to distinguish. load xxx::myfile.whatever xxx:: is a file type, such as MOL; followed by two colons. faster loading (maybe) ---------------------- Jmol 11.1.30 uses a much more efficient mechanism for file loading. Let us know if it works. As part of this work the JAR files were realigned and have new names: *JmolApplet0.jar *JmolAppletCore.jar *JmolAppletJars.jar *JmolAppletJvxl.jar *JmolAppletMain.jar *JmolAppletPopup.jar *JmolAppletViewer.jar JmolAppletQuantum.jar JmolAppletReadersCifPdb.jar JmolAppletReadersMolXyz.jar JmolAppletReadersMore.jar JmolAppletReadersXml.jar JmolAppletShapeBio.jar JmolAppletShapeSpecial.jar JmolAppletSmiles.jar JmolApplet_i18n.jar (translations) *required (650 Kb) JmolApplet0.jar is still there, but the other six are replaced by the above list, which are loaded only as needed and can even be left off a site (though that is not recommended) if not used. So, for example, if you never use molecular orbitals, they will never be there; if you never use biomolecular cartoons, your user will never have them downloaded. The required download is now about 650 Kb, only about 80% of the size of Jmol 10.2. The first time you use "cartoon on", for example, the ShapeBio package is delivered. This means that there could be noticeable delays later in the loading process. If this does not suit you, just use JmolApplet.jar; it's size (1M) is still only about 75% of the size of 11.1.29 and only 22% larger than Jmol 10.2. ----------------------------------- That's all for 11.1.30 Bob Hanson 
 Re: [Jmol-users] Jmol 11.1.30 From: Nicolas Vervelle - 2007-05-03 21:17:38 Bob Hanson wrote: > Jmol 11.1.30 is ready for release, Nico. > See my other mail, there's a bug somewhere when running monster_script.spt. Can you fix it before I release 11.1.30 ? Nico 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2007-05-04 06:23:05 Thanks, Craig. That's just what I needed. Craig T Martin wrote: > Bob, > > As someone else pointed out, i think, when you access the signed > applet, it will ask you for permission to run. A dialog will pop up > before Jmol fully loads. If you get that dialog, and then everything > after that goes smoothly, then the signed applet is working. > > It will only ask you once per session. To see the request again, > you'll have to quit your browser and then reopen. > > You can pull down a test that when run locally should automatically > run the trusted applet at: > > ; > > Craig > > Craig Martin > cmartin@... > > > > On May 3, 2007, at 11:31 AM, Bob Hanson wrote: > >> Craig T Martin wrote: >> >>>> Message: 3 >>>> Date: Wed, 02 May 2007 19:14:11 -0500 >>>> From: Bob Hanson >>>> > >>>> Subject: [Jmol-users] signed applets >>>> To: jmol-users@... >>>> >>>> >>>> Message-ID: <46392953.9090809@... >>>> >>>> > >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> I looking for someone who is using the signed applet. >>> >>> >>> >>> Dear Bob, >>> >>> I use it all the time, though only for local file access, not >>> from one server to another. >>> >>> In my usage, i have a javascript that figures out if the access is >>> local or to a server. If the former, then it uses the signed applet. >>> Thus all of my local development is with the signed applet. >>> >>> However, I've had a hard time keeping up with the (fantastic) pace >>> of your development. The most recent version I've used is 10.9.98. >>> The signed applet works great with that (on a Mac, usually Safari). >>> >>> Did you have a specific question? >>> >> Yes. What should I do to test that I have the signed applet working? >> >>> Craig >>> >>> Craig Martin >>> cmartin@... >>> >>> >>> >>> >> > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > 
 Re: [Jmol-users] Jmol 11.1.30 From: Angel Herraez - 2007-05-03 23:41:02 Bob Hanson wrote: > Jmol 11.1.30 is ready for release, Nico. > load =3Dxxxx Impressive! > OK, features. Not too many: Not too many? You MUST be kidding! > full support for switching languages, including a new "language" menu it= em > ------------------------------------------------------------------------= --- > Now you can switch languages anytime you want. Just pop up the menu and > select > the new "language" item near the bottom. This is heaven! > WE NEED PEOPLE TO VOLUNTEER TO DO MORE TRANSLATIONS, even in just the > set of languages we are supporting. It would be nice just to get that > menu put translation done. Someone want to work on this? Not sure what you mean: translating the new "language" menu entry itself? Oh, I see. We have all names of available languages as sub-entries in that= menu. I am about to translate them all into Spanish for es.po, but not sure it is a good id= ea. Shouldn't we have each one fixed in its own language, independently of the locale? I mean, If I am French and the menu opens in English, I'd rather recognize= "Fran=E7ais" than "French". Or, if Bob opens Jmol in a Spanish computer, and wants his Engli= sh menus, will he prefer seeing "English" or "Ingl=E9s" --well, Bob is not a good example, h= e can recongize Spanish words ;-) What are your views? > Pqr reader > ---------- > Jmol now reads Pqr data files created using PDB2PQR No need to use the file type forcing ? 
 [Jmol-users] (no subject) From: Benny Chain - 2007-09-02 08:48:24 Attachments: Message as HTML Does anyone know if it is possible to define a file name (for example to save an image) as a variable , so that one can automatically move from file to file in a looping script ? Or is there any other way to save repeated images not in the same file during script execution ? Benny Chain Benjamin Chain Department of Immunology and Molecular Pathology Windeyer Institute of Medical Sciences UCL, 46 Cleveland St. London W1T 4JF Fax 00 44 20 7679 9301 
 Re: [Jmol-users] file name from variable [was: (no subject)] From: Angel Herraez - 2007-09-02 10:27:56 Hello Benny I'm quite sure it can be done using Jmol math, but I have no experience wth that. I would say there have been posts regarding this; do a search in the list archive, possibly for "animated images" which was a frequent discussion topic. > Does anyone know if it is possible to define a file name (for example to save an image) as > a variable , so that one can automatically move from file to file in a looping script ? Or is > there any other way to save repeated images not in the same file during script execution ? > > Benny Chain 
 Re: [Jmol-users] file name from variable [was: (no subject)] From: Bob Hanson - 2007-09-02 14:21:50 Jmol math: x = "myfile.xyz" load @x Angel Herraez wrote: >Hello Benny > >I'm quite sure it can be done using Jmol math, but I have no experience wth that. >I would say there have been posts regarding this; do a search in the list archive, possibly for >"animated images" which was a frequent discussion topic. > > > >>Does anyone know if it is possible to define a file name (for example to save an image) as >>a variable , so that one can automatically move from file to file in a looping script ? Or is >>there any other way to save repeated images not in the same file during script execution ? >> >>Benny Chain >> >> > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 [Jmol-users] (no subject) From: Eran Hodis - 2007-10-11 13:08:23 Dear Jmol Users, In addition to my question yesterday concerning the total number of atoms selected, I have another question I hope you can lend your expertise to: I'd like to save a state as a script in such a way that when that state-script is recalled on a Jmol applet already displaying something, that state-script will load without affecting the spin- state of the applet -- that is, if the applet has spin on before loading the state-script, then spin stays on, and if spin was off prior to loading the state-script, then spin stays off. Any ideas? Best, Eran 
 Re: [Jmol-users] (no subject) From: - 2007-10-11 14:11:35 Attachments: Message as HTML Eran wrote: > I'd like to save a state as a script in such a way that when that =20 > state-script is recalled on a Jmol applet already displaying =20 > something, that state-script will load without affecting the spin-=20 > state of the applet=20 Hello Easiest way: if the script is saved to a file, edit it and remove the = spin command from the state-script. Otherwise, I think you can use "show spin" to read the spin state before = calling the state, then issue it after the script. I did something similar for a "Foolproof spin toggle" you can see at http://wiki.jmol.org:81/index.php/Recycling_Corner#.22Foolproof.22_spin_t= oggle That may give you an idea. 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2007-10-12 16:25:57 Herráez Sánchez Angel wrote: >Eran wrote: > > >>I'd like to save a state as a script in such a way that when that >>state-script is recalled on a Jmol applet already displaying >>something, that state-script will load without affecting the spin- >>state of the applet >> >> > >Hello > >Easiest way: if the script is saved to a file, edit it and remove the spin command from the state-script. > > > won't work -- loading the file resets any spinning, and you can't . >Otherwise, I think you can use "show spin" to read the spin state before calling the state, then issue it after the script. > > that's the way to do it. JavaScript: var spinState = jmolEvaluate('script("show spin")')) gets you something like: spinX = 0;spinY = 30;spinZ = 0;spinFps = 30; spin 20.0 {2.3090453 0.0 0.0} {1.3767258 1.136295 0.6437832}; which can then later be used. or Jmol script, not JavaScript: spinState = script("show spin"); script "mysavedstate.spt"; print script(spinState); The "print" doesn't do anything, but it allows the script now saved in spinState to be executed. >I did something similar for a "Foolproof spin toggle" you can see at >http://wiki.jmol.org:81/index.php/Recycling_Corner#.22Foolproof.22_spin_toggle >That may give you an idea. > > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 [Jmol-users] (no subject) From: Eran Hodis - 2007-10-11 17:00:50 It appears that saving a state in Jmol does not save the backbone setting. Is there a way I can make the state save the backbone setting, or alternatively, ask Jmol "what is the backbone setting" so that my code can add the backbone setting automatically to the saved state? Thank you, Eran Hodis 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2007-10-12 21:39:57 Hmm. Backbone is a particularly difficult one to save in a state. The simple idea I tried did not work, so I will experiment some more. I don't have time right now to come up with a solution. Eran Hodis wrote: >It appears that saving a state in Jmol does not save the backbone >setting. > >Is there a way I can make the state save the backbone setting, or >alternatively, ask Jmol "what is the backbone setting" so that my >code can add the backbone setting automatically to the saved state? > >Thank you, >Eran Hodis > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2007-10-12 21:40:04 Eran Hodis wrote: >It appears that saving a state in Jmol does not save the backbone >setting. > >Is there a way I can make the state save the backbone setting, or >alternatively, ask Jmol "what is the backbone setting" so that my >code can add the backbone setting automatically to the saved state? > > > that would be a bug. I'll look into it. >Thank you, >Eran Hodis > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2007-10-14 03:57:31 this is fixed and should show up in the next release. Eran Hodis wrote: >It appears that saving a state in Jmol does not save the backbone >setting. > >Is there a way I can make the state save the backbone setting, or >alternatively, ask Jmol "what is the backbone setting" so that my >code can add the backbone setting automatically to the saved state? > >Thank you, >Eran Hodis > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 [Jmol-users] (no subject) From: Jonathan Ouellet - 2007-12-05 13:00:13 Attachments: Message as HTML Hi, I would like to overlay a density map over a pdb model in Jmol so that I could happily put it on the web. However, I saw that Jmol handle only gaussian cube density maps. Unfortunately, I don't have access to that expensive software (and I don't really know what it is). I was wondering if there is a way to convert to .cub, or ideally, insert a CCP4 or xplor density map in Jmol ? cheers jo 
 Re: [Jmol-users] (no subject) From: Bob Hanson - 2007-12-05 18:21:07 Jonathan Ouellet wrote: > Hi, > > > I would like to overlay a density map over a pdb model in Jmol so that > I could happily put it on the web. > > However, I saw that Jmol handle only gaussian cube density maps. > > Unfortunately, I don't have access to that expensive software (and I > don't really know what it is). > > I was wondering if there is a way to convert to .cub, or ideally, > insert a CCP4 or xplor density map in Jmol ? I'd love to get CCP4 or explor density maps in Jmol. Send me some sample files -- the PDB model, the density maps, any information you have about format -- and I will do it. Bob > > > cheers > > jo > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >SF.Net email is sponsored by: The Future of Linux Business White Paper >from Novell. From the desktop to the data center, Linux is going >mainstream. Let it simplify your IT future. >http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 [Jmol-users] jmol and Xplor electron density maps From: Bob Hanson - 2007-12-06 07:22:38 I have a little XPLOR ascii-format electron density map reader worked out. Can someone send me a few files? I need a molecular coordinate file and the corresponding Xplor electron density map. I'm not sure exactly what the file format description is telling me: Example format for Xplor Maps: 2 !NTITLE REMARKS FILENAME="" REMARKS scitbx.flex.double to Xplor map format 24 0 24 120 0 120 54 0 54 3.20420E+01 1.75362E+02 7.96630E+01 9.00000E+01 9.00000E+01 9.00000E+01 ZYX 0 -2.84546E-01-1.67775E-01-5.66095E-01-1.18305E+00-1.49559E+00-1.31942E+00 -1.01611E+00-1.00873E+00-1.18992E+00-1.02460E+00-2.72099E-01 5.94242E-01 -9999 0.0000E+00 1.0000E+00 That is: ...a blank line ...an integer giving the number of title lines, with mandatory !NTITLE ...title lines in %-264s format ...X, Y, and Z sections giving: N sections per unit cell, in the given direction Nmin ordinal of first section in file Nmax ordinal of last section in file [so, is a section a point, or are there N+1 points for N sections?] [what if the first ordinal is not 0? What does that mean?] [is it always true that Nmin + N = Nmax ?] ...unit cell dimensions [do these have to be orthogonal? (I'm guessing not --- doesn't matter to me, just wondering)] ...slow, medium, fast section order, always ZYX [happy about that] ...for each slow section, the section number ...sectional data in special fortran format shown [looks simple enough to me] ...-9999 ...map average and standard deviation Bob Hanson wrote: >Jonathan Ouellet wrote: > > > >>Hi, >> >> >>I would like to overlay a density map over a pdb model in Jmol so that >>I could happily put it on the web. >> >>However, I saw that Jmol handle only gaussian cube density maps. >> >>Unfortunately, I don't have access to that expensive software (and I >>don't really know what it is). >> >>I was wondering if there is a way to convert to .cub, or ideally, >>insert a CCP4 or xplor density map in Jmol ? >> >> > > >I'd love to get CCP4 or explor density maps in Jmol. > >Send me some sample files -- the PDB model, the density maps, any >information you have about format -- and I will do it. > >Bob > > > >>cheers >> >>jo >> >> >>------------------------------------------------------------------------ >> >>------------------------------------------------------------------------- >>SF.Net email is sponsored by: The Future of Linux Business White Paper >> >> >>from Novell. From the desktop to the data center, Linux is going > > >>mainstream. Let it simplify your IT future. >>http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>Jmol-users mailing list >>Jmol-users@... >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> > > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] jmol and Xplor electron density maps From: Angel Herraez - 2007-12-06 09:23:35 On 6 Dec 2007 at 1:22, Bob Hanson wrote: > I have a little XPLOR ascii-format electron density map reader worked > out. Can someone send me a few files? > I need a molecular coordinate file and the corresponding Xplor electron > density map. I don't work with that, but I found these docs that might help you: http://www.ocms.ox.ac.uk/mirrored/xplor/manual/htmlman/node312.html#S ECTION0015300000000000000 http://www.bio.net/hypermail/x-plor/1996-January/000325.html http://linkinghub.elsevier.com/retrieve/pii/S0969212605000626 (the article refers to software at http://www.scripps.edu/~sanner/software ) HTH, 
 Re: [Jmol-users] jmol and Xplor electron density maps From: Bob Hanson - 2007-12-06 13:52:52 OK, the next version of Jmol (11.3.53) reads Xplor ASCII format electron density maps for isosurface creation and for mapping. (Object-oriented programming works! The whole thing is only about 100 lines of code.) Here's my question: How do you use this sort of data? Do you create an isosurface from it and visualize it directly? Do you use it to map color onto another surface? Do people do both? Usually one, usually the other? The reason I ask is that the sample file I found had a 132x132x96 grid, and that was just way too much for Jmol. But there may be a general solution to large data sets that will work. It will be an interesting challenge to stream this data set and see if we can compress it into JVXL format on the fly. I think I know how to do that, but it's not a simple afternoon project, not like writing that reader. Angel Herraez wrote: >On 6 Dec 2007 at 1:22, Bob Hanson wrote: > > > >>I have a little XPLOR ascii-format electron density map reader worked >>out. Can someone send me a few files? >>I need a molecular coordinate file and the corresponding Xplor electron >>density map. >> >> > >I don't work with that, but I found these docs that might help you: > >http://www.ocms.ox.ac.uk/mirrored/xplor/manual/htmlman/node312.html#S >ECTION0015300000000000000 > >http://www.bio.net/hypermail/x-plor/1996-January/000325.html > >http://linkinghub.elsevier.com/retrieve/pii/S0969212605000626 >(the article refers to software at http://www.scripps.edu/~sanner/software ) > > >HTH, > > > >------------------------------------------------------------------------- >SF.Net email is sponsored by: The Future of Linux Business White Paper >from Novell. From the desktop to the data center, Linux is going >mainstream. Let it simplify your IT future. >http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 [Jmol-users] (no subject) From: Mike Miller - 2007-12-19 10:28:02 Attachments: Message as HTML H, Please include me in the list, Mike 
 Re: [Jmol-users] (no subject) From: Egon Willighagen - 2007-12-19 10:32:02 On Dec 19, 2007 11:38 AM, Mike Miller wrote: > Please include me in the list, You should be subscribed now. Egon -- ---- http://chem-bla-ics.blogspot.com/ 
 [Jmol-users] (no subject) From: David Leader - 2008-04-07 13:02:15 Attachments: Message as HTML Green links work fine on Safari 3.1 and Firefox 2 on Mac OS X 10.4.11 and 10.5.2 for 1eve. David ___________________________________________________ Dr. David P.Leader, Biochemistry and Molecular Biology, FBLS, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader ___________________________________________________ 
 [Jmol-users] (no subject) From: Kathy - 2008-12-02 03:49:36 Please remove me from the mailing list. This is not what I thought it was. 
 Re: [Jmol-users] (no subject) From: Egon Willighagen - 2008-12-02 06:59:15 On Tue, Dec 2, 2008 at 5:00 AM, Kathy wrote: > Please remove me from the mailing list. This is not what I thought it was. You can unsubscribe at: https://lists.sourceforge.net/lists/listinfo/jmol-users Egon -- ---- http://chem-bla-ics.blogspot.com/ 
 [Jmol-users] (no subject) From: Kathy - 2009-02-02 00:13:40 Please remove me from the mailing list. 
 Re: [Jmol-users] (no subject) From: Egon Willighagen - 2009-02-02 05:55:34 Dear Kathy, On Mon, Feb 2, 2009 at 1:26 AM, Kathy wrote: > Please remove me from the mailing list. please visit: https://lists.sourceforge.net/lists/listinfo/jmol-users where you can unsubscribe yourself. Kind regards, Egon -- ---- http://chem-bla-ics.blogspot.com/ 
 [Jmol-users] (no subject) From: Fred Ziegler - 2009-04-29 13:17:02 To Those in the Know: I would like to display an electrostatic potential map with a white background rather than the default black. While this code --------
-------- works, it loads in black first. Is there a way to load directly in white? Fred ziegler -- **************************************** Professor Frederick E. Ziegler, Emeritus Sterling Chemistry Laboratory 225 Prospect Street Yale University P.O. Box 208107 New Haven, Connecticut 06520-8107 E-mail: frederick.ziegler@... Telephone: (203) 432-3959 Fax: (203) 432-6144 **************************************** 
 Re: [Jmol-users] (no subject) From: Angel Herráez - 2009-04-29 21:34:26 Hi Fred I understand that your problem is not specific to the electrostatic potential surface, but just to the background color appearing momentarily in black. Since the isosurface takes some time to load, there may be a delay causing the black color to remain visible. Two things you can try (I bet that nr. 2 will be better than nr.1): 1. insert a "refresh" command after "color background white", so that Jmol updates the display before starting to load the isosurface. 2. Use jmolSetAppletColor, which prepares the applet parameters before it is inserted: jmolInitialize( etc ) jmolSetAppletColor("white") jmolApplet(200,'load etc 
 Re: [Jmol-users] (no subject) From: Fred Ziegler - 2009-04-30 01:51:32 >Angel: I figured it out after i sent the e-mail. Thanks, Fred >Hi Fred > >I understand that your problem is not specific to the electrostatic potential >surface, but just to the background color appearing momentarily in black. >Since the isosurface takes some time to load, there may be a delay >causing the black color to remain visible. >Two things you can try (I bet that nr. 2 will be better than nr.1): > >1. insert a "refresh" command after "color background white", so that Jmol >updates the display before starting to load the isosurface. > >2. Use jmolSetAppletColor, which prepares the applet parameters before it >is inserted: > >jmolInitialize( etc ) >jmolSetAppletColor("white") >jmolApplet(200,'load etc > > > >------------------------------------------------------------------------------ >Register Now & Save for Velocity, the Web Performance & Operations >Conference from O'Reilly Media. Velocity features a full day of >expert-led, hands-on workshops and two days of sessions from industry >leaders in dedicated Performance & Operations tracks. Use code vel09scf >and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users -- **************************************** Professor Frederick E. Ziegler, Emeritus                         Sterling Chemistry Laboratory  225 Prospect Street Yale University          P.O. Box 208107      New Haven, Connecticut 06520-8107     E-mail: frederick.ziegler@...  Telephone: (203) 432-3959              Fax: (203) 432-6144                    **************************************** 
 [Jmol-users] (no subject) From: Alejandro Rangel López - 2009-07-29 06:35:21 i need info about how to use jmol program i've only opened the jmol.jar but then i dunno wut to do 
 [Jmol-users] (no subject) From: Durga Bhavani Kuchibhatla - 2009-08-14 02:13:10 Attachments: Message as HTML Hello, Iam new to jmol. Can u pls tell me how to load pdb files with file extension .ent.Z into jmol applet. When I try to load pdb files with this extension, the browser crashes( error: unrecognized file type) . Please help Thanks 
 Re: [Jmol-users] loading Z files [was: (no subject)] From: Angel Herráez - 2009-08-14 09:37:54 Attachments: Message as HTML Hello Durga > Iam new to jmol. Can u pls tell me how to load pdb files with file extension .ent.Z into jmol > applet. Jmol can load uncompressed (plain text), gzipped or zipped files, but not Z-compressed files. You will have to use another version of the pdb files, for example the .ent file or a .gz version. > When I try to load pdb files with this extension, the browser crashes( error: unrecognized > file type) . I hope that is NOT a browser crash, but only a Jmol error that ends the action. The browser should still be responsive, is it not? 
 Re: [Jmol-users] loading Z files [was: (no subject)] From: Durgabhavani Kuchibhatla - 2009-08-15 01:12:15 Attachments: Message as HTML Hi Angel, Thanks for your reply. When I tried to load .Z file , all the open browser windows completely closed down. (I was working with firefox). I loaded the uncompressed file and it is working fine. Thanks once again Durga From: angel.herraez@... To: jmol-users@... Date: Fri, 14 Aug 2009 11:50:02 +0200 Subject: Re: [Jmol-users] loading Z files [was: (no subject)] Hello Durga > Iam new to jmol. Can u pls tell me how to load pdb files with file extension .ent.Z into jmol > applet. Jmol can load uncompressed (plain text), gzipped or zipped files, but not Z-compressed files. You will have to use another version of the pdb files, for example the .ent file or a .gz version. > When I try to load pdb files with this extension, the browser crashes( error: unrecognized > file type) . I hope that is NOT a browser crash, but only a Jmol error that ends the action. The browser should still be responsive, is it not? _________________________________________________________________ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx
 [Jmol-users] (no subject) From: Edgar Luttmann - 2009-11-09 20:06:58 Attachments: Message as HTML Hi, I am using JMol to display an animation with surfaces. For performance issues I precalculate those surface and store them as jvxl files. One sample animation consists of 41 frames and currently I need to load 41 jvxl surfaces for this to work. So I am wondering if there is a way to merge all precalculated surfaces into a single file and load that file within JMol. Thanks for any hints and cheers, Edgar 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2009-11-09 21:59:49 Attachments: Message as HTML Well, sort of. You can store multiple surfaces in a single JVXL file, but right now there's no way to read them all into different frames all at once. However, since the browser will cache the files, you might want to try that. I haven't worked out a way to write a set of surfaces to a file, so you would have to construct this file manually, cutting and pasting. Probably not a solution for you. But it's not terribly difficult. The negative number on the "35 90 Jmol voxel format" line tells how many surfaces are in the file. Then the data are just appended: -2 35 90 Jmol voxel format version 0.9 0.03 1318 1114 compressionRatio=416.05264 25704 1 38 ... 34 5 35 5 35 5 36 3 38 1 25695 $x#(]>:Fd;VX_3R... -0.03 1317 1102 compressionRatio=418.28854 25695 2 37 3...5 5 35 5 36 3 38 1 25704 #x#%iA=FX8... You would still have to do something like: frame 1;isosurface "myfile.jvxl" 1 frame 2;isosurface "myfile.jvxl" 2 etc. I know, not a great solution. Bob On Mon, Nov 9, 2009 at 2:06 PM, Edgar Luttmann wrote: > Hi, > > I am using JMol to display an animation with surfaces. For performance > issues I precalculate those surface and store them as jvxl files. One sample > animation consists of 41 frames and currently I need to load 41 jvxl > surfaces for this to work. > > So I am wondering if there is a way to merge all precalculated surfaces > into a single file and load that file within JMol. > > Thanks for any hints and cheers, > Edgar > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900   Re: [Jmol-users] jvxl From: Edgar Luttmann - 2009-11-11 14:39:56 Attachments: Message as HTML Thanks Robert. I will try that and sorry for the missing subject. Cheers, Ed --- On Mon, 11/9/09, Robert Hanson wrote: From: Robert Hanson Subject: Re: [Jmol-users] (no subject) To: jmol-users@... Date: Monday, November 9, 2009, 1:59 PM Well, sort of. You can store multiple surfaces in a single JVXL file, but right now there's no way to read them all into different frames all at once. However, since the browser will cache the files, you might want to try that. I haven't worked out a way to write a set of surfaces to a file, so you would have to construct this file manually, cutting and pasting. Probably not a solution for you. But it's not terribly difficult. The negative number on the "35 90 Jmol voxel format" line tells how many surfaces are in the file. Then the data are just appended: -2 35 90 Jmol voxel format version 0.9 0.03 1318 1114 compressionRatio=416.05264 25704 1 38 ... 34 5 35 5 35 5 36 3 38 1 25695$x#(]>:Fd;VX_3R... -0.03 1317 1102 compressionRatio=418.28854  25695 2 37 3...5 5 35 5 36 3 38 1 25704 #x#%iA=FX8... You would still have to do something like: frame 1;isosurface "myfile.jvxl" 1 frame 2;isosurface "myfile.jvxl" 2 etc. I know, not a great solution. Bob On Mon, Nov 9, 2009 at 2:06 PM, Edgar Luttmann wrote: Hi, I am using JMol to display an animation with surfaces. For performance issues I precalculate those surface and store them as jvxl files. One sample animation consists of 41 frames and currently I need to load 41 jvxl surfaces for this to work. So I am wondering if there is a way to merge all precalculated surfaces into a single file and load that file within JMol. Thanks for any hints and cheers, Edgar ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now.  http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-users mailing list Jmol-users@... https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -----Inline Attachment Follows----- ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now.  http://p.sf.net/sfu/bobj-july -----Inline Attachment Follows----- _______________________________________________ Jmol-users mailing list Jmol-users@... https://lists.sourceforge.net/lists/listinfo/jmol-users 
 [Jmol-users] (no subject) From: P.Canepa - 2010-04-15 11:01:07 Attachments: Message as HTML Dear all, In the page I am working on I create a button to load new files as below: function loadModels() is expected to load on an external list all the models called within the first JmolScript(load ? .... ). loadModels() just reads models from the previous structure and not from the latest. Do you know how to solve his problem? Does exist a way to let the javascript be executed sequentially as they are written? for instance jmolScript("load ?; script scripts/name.spt; background white") + removeAllModels() + loadModels() . Stick to the sequence .... Thanks a lot, Piero Function loadModels() is function loadModels(selectbox){ var Info = jmolGetPropertyAsArray("auxiliaryInfo.models") if(!Info){ alert("No models available") return } for(var i=0; i< Info.length; i++) addOption(document.modelsVib.models, i + " " + Info[i].name, i + 2); } function addOption(selectbox,text,value) { var optn = document.createElement("OPTION"); optn.text = text; optn.value = value; selectbox.options.add(optn); } thanks, Piero -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2010-04-15 11:30:53 Attachments: Message as HTML  OnClick='jmolScript("load ?; script scripts/name.spt; background white") + removeAllModels() + loadModels()' adds function returns in JavaScript. I think you want semicolons. Generally good programming is to only have a single function in the onclick: OnClick='onClickLoadStruc()' and then function onClickLoadStruc() { jmolScript("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } Remember that jmolScript() is asynchronous -- it queues the load command but continues immediately. You want: function onClickLoadStruc() { jmolScriptWait("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } Bob Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: P.Canepa - 2010-04-15 12:05:58 Attachments: Message as HTML The last one doesn't work. It comes up with an error JmolApplet0,,, Zapped! why ? Thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Robert Hanson [hansonr@...] Sent: Thursday, April 15, 2010 12:30 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) OnClick='jmolScript("load ?; script scripts/name.spt; background white") + removeAllModels() + loadModels()' adds function returns in JavaScript. I think you want semicolons. Generally good programming is to only have a single function in the onclick: OnClick='onClickLoadStruc()' and then function onClickLoadStruc() { jmolScript("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } Remember that jmolScript() is asynchronous -- it queues the load command but continues immediately. You want: function onClickLoadStruc() { jmolScriptWait("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } Bob Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2010-04-15 12:44:45 Attachments: Message as HTML what last one doesn't, and what comes up with what sort of error? On Thu, Apr 15, 2010 at 7:02 AM, P.Canepa wrote: > The last one doesn't work. It comes up with an error JmolApplet0,,, > Zapped! why ? > > Thanks > > -- > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc229@... > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > ------------------------------ > *From:* Robert Hanson [hansonr@...] > *Sent:* Thursday, April 15, 2010 12:30 PM > > *To:* jmol-users@... > *Subject:* Re: [Jmol-users] (no subject) > > OnClick='jmolScript("load ?; script scripts/name.spt; background > white") + removeAllModels() + loadModels()' > > adds function returns in JavaScript. I think you want semicolons. Generally > good programming is to only have a single function in the onclick: > > OnClick='onClickLoadStruc()' > > > and then > > function onClickLoadStruc() { > jmolScript("load ?; script scripts/name.spt; background white") > removeAllModels() > loadModels() > } > > Remember that jmolScript() is asynchronous -- it queues the load command > but continues immediately. You want: > > function onClickLoadStruc() { > jmolScriptWait("load ?; script scripts/name.spt; background white") > removeAllModels() > loadModels() > } > > Bob > > > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: P.Canepa - 2010-04-15 14:21:08 Attachments: Message as HTML Dear Bob, I tried this one because it looks to me the more feasible. This gives me that error I told you. Thanks Piero function onClickLoadStruc() { jmolScriptWait("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Robert Hanson [hansonr@...] Sent: Thursday, April 15, 2010 1:44 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) what last one doesn't, and what comes up with what sort of error? On Thu, Apr 15, 2010 at 7:02 AM, P.Canepa > wrote: The last one doesn't work. It comes up with an error JmolApplet0,,, Zapped! why ? Thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Robert Hanson [hansonr@...] Sent: Thursday, April 15, 2010 12:30 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) OnClick='jmolScript("load ?; script scripts/name.spt; background white") + removeAllModels() + loadModels()' adds function returns in JavaScript. I think you want semicolons. Generally good programming is to only have a single function in the onclick: OnClick='onClickLoadStruc()' and then function onClickLoadStruc() { jmolScript("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } Remember that jmolScript() is asynchronous -- it queues the load command but continues immediately. You want: function onClickLoadStruc() { jmolScriptWait("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } Bob Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list Jmol-users@... https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: P.Canepa - 2010-04-15 14:36:48 Attachments: Message as HTML Te error I see on the jmol deck is java.Security.AccessControlException: access.denied (java.io.FilePermission ... this happens per each file? How comes ? all the best, Piero -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: P.Canepa [pc229@...] Sent: Thursday, April 15, 2010 3:19 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) Dear Bob, I tried this one because it looks to me the more feasible. This gives me that error I told you. Thanks Piero function onClickLoadStruc() { jmolScriptWait("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Robert Hanson [hansonr@...] Sent: Thursday, April 15, 2010 1:44 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) what last one doesn't, and what comes up with what sort of error? On Thu, Apr 15, 2010 at 7:02 AM, P.Canepa > wrote: The last one doesn't work. It comes up with an error JmolApplet0,,, Zapped! why ? Thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Robert Hanson [hansonr@...] Sent: Thursday, April 15, 2010 12:30 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) OnClick='jmolScript("load ?; script scripts/name.spt; background white") + removeAllModels() + loadModels()' adds function returns in JavaScript. I think you want semicolons. Generally good programming is to only have a single function in the onclick: OnClick='onClickLoadStruc()' and then function onClickLoadStruc() { jmolScript("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } Remember that jmolScript() is asynchronous -- it queues the load command but continues immediately. You want: function onClickLoadStruc() { jmolScriptWait("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } Bob Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list Jmol-users@... https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Paul Pillot - 2010-04-15 14:54:36 Attachments: Message as HTML make sure the applet and the files are located in the same directory. Paul Le 15 avr. 2010 à 16:34, P.Canepa a écrit : > Te error I see on the jmol deck is java.Security.AccessControlException: access.denied (java.io.FilePermission ... > this happens per each file? How comes ? > > all the best, Piero > > -- 
 Re: [Jmol-users] (no subject) From: P.Canepa - 2010-04-15 14:58:11 Attachments: Message as HTML It's strange because all work if I use the normal jmolScript as below function onClickLoadStruc() { jmolScript("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } This just happens when I employ jmolScriptWait(....) -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Paul Pillot [paul.pillot@...] Sent: Thursday, April 15, 2010 3:54 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) make sure the applet and the files are located in the same directory. Paul Le 15 avr. 2010 à 16:34, P.Canepa a écrit : Te error I see on the jmol deck is java.Security.AccessControlException: access.denied (java.io.FilePermission ... this happens per each file? How comes ? all the best, Piero -- 
 Re: [Jmol-users] (no subject) From: P.Canepa - 2010-04-15 15:30:11 Attachments: Message as HTML I realized that the file is correctly read with jmolScript("load ? ") wherever it is, whereas it has to be in the same directory as the applet if the command jmolScriptWait("load ? ") . Why ? How can I solve it ? What I am tiring to do is an online visualizer. So I cannot set a set ; defaultDirectory as the user browses the file he likes. Thanks -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: P.Canepa [pc229@...] Sent: Thursday, April 15, 2010 3:56 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) It's strange because all work if I use the normal jmolScript as below function onClickLoadStruc() { jmolScript("load ?; script scripts/name.spt; background white") removeAllModels() loadModels() } This just happens when I employ jmolScriptWait(....) -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Paul Pillot [paul.pillot@...] Sent: Thursday, April 15, 2010 3:54 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) make sure the applet and the files are located in the same directory. Paul Le 15 avr. 2010 à 16:34, P.Canepa a écrit : Te error I see on the jmol deck is java.Security.AccessControlException: access.denied (java.io.FilePermission ... this happens per each file? How comes ? all the best, Piero -- 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2010-04-15 15:30:37 Attachments: Message as HTML Ah, ok. I remember. You are getting an access violation because the thread that runs the load command cannot also run the JavaScript command. Problem: I want to load a file using the dialog in the signed applet and then after that run some JavaScript. Solution: You must use the message callback mechanism to let your page know that the loading is done, and from THAT function, run your JavaScript: function loadModels(){ removeAllModels() var Info = jmolGetPropertyAsArray("auxiliaryInfo.models") .. etc... } function myMessageCallback(a,m) { m = "" + m // important to do this to change from Java string to JavaScript string if (m.indexOf("DONE") == 0) loadModels() } function onClickLoadStruc() { jmolScript("load ?; background white;set messageCallback 'myMessageCallback';message DONE") } Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: P.Canepa - 2010-04-15 15:42:58 Attachments: Message as HTML Are you sure because nothing seems to change! -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Robert Hanson [hansonr@...] Sent: Thursday, April 15, 2010 4:30 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) Ah, ok. I remember. You are getting an access violation because the thread that runs the load command cannot also run the JavaScript command. Problem: I want to load a file using the dialog in the signed applet and then after that run some JavaScript. Solution: You must use the message callback mechanism to let your page know that the loading is done, and from THAT function, run your JavaScript: function loadModels(){ removeAllModels() var Info = jmolGetPropertyAsArray("auxiliaryInfo.models") .. etc... } function myMessageCallback(a,m) { m = "" + m // important to do this to change from Java string to JavaScript string if (m.indexOf("DONE") == 0) loadModels() } function onClickLoadStruc() { jmolScript("load ?; background white;set messageCallback 'myMessageCallback';message DONE") } Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: P.Canepa - 2010-04-15 15:46:47 Attachments: Message as HTML Quick mind Bob my functions are. Then what's wrong ? Thanks, Piero function loadModels(selectbox){ removeAllModels() var Info = jmolGetPropertyAsArray("auxiliaryInfo.models") if(!Info){ alert("No models available") return } for(var i=0; i< Info.length; i++) addOption(document.modelsVib.models, i + " " + Info[i].name, i + 2); } function myMessageCallback(a,m) { m = "" + m // important to do this to change from Java string to JavaScript string if (m.indexOf("DONE") == 0) loadModels() } function onClickLoadStruc() { jmolScriptWait("load ?; background white; set messageCallback 'myMessageCallback';message DONE"); } -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: P.Canepa [pc229@...] Sent: Thursday, April 15, 2010 4:42 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) Are you sure because nothing seems to change! -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________ From: Robert Hanson [hansonr@...] Sent: Thursday, April 15, 2010 4:30 PM To: jmol-users@... Subject: Re: [Jmol-users] (no subject) Ah, ok. I remember. You are getting an access violation because the thread that runs the load command cannot also run the JavaScript command. Problem: I want to load a file using the dialog in the signed applet and then after that run some JavaScript. Solution: You must use the message callback mechanism to let your page know that the loading is done, and from THAT function, run your JavaScript: function loadModels(){ removeAllModels() var Info = jmolGetPropertyAsArray("auxiliaryInfo.models") .. etc... } function myMessageCallback(a,m) { m = "" + m // important to do this to change from Java string to JavaScript string if (m.indexOf("DONE") == 0) loadModels() } function onClickLoadStruc() { jmolScript("load ?; background white;set messageCallback 'myMessageCallback';message DONE") } Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2010-04-15 16:08:45 Attachments: Message as HTML show me the page. On Thu, Apr 15, 2010 at 10:45 AM, P.Canepa wrote: > Quick mind Bob > my functions are. Then what's wrong ? > > Thanks, Piero > > function loadModels(selectbox){ > > removeAllModels() > var Info = jmolGetPropertyAsArray("auxiliaryInfo.models") > > if(!Info){ > alert("No models available") > return > } > > for(var i=0; i< Info.length; i++) > addOption(document.modelsVib.models, i + " " + Info[i].name, i + 2); > } > > function myMessageCallback(a,m) { > m = "" + m > // important to do this to change from Java string to JavaScript string > if (m.indexOf("DONE") == 0) loadModels() > } > > function onClickLoadStruc() { > jmolScriptWait("load ?; background white; set messageCallback'myMessageCallback';messageDONE"); > } > > -- > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc229@... > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > ------------------------------ > *From:* P.Canepa [pc229@...] > *Sent:* Thursday, April 15, 2010 4:42 PM > > *To:* jmol-users@... > *Subject:* Re: [Jmol-users] (no subject) > > Are you sure because nothing seems to change! > > -- > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc229@... > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > ------------------------------ > *From:* Robert Hanson [hansonr@...] > *Sent:* Thursday, April 15, 2010 4:30 PM > *To:* jmol-users@... > *Subject:* Re: [Jmol-users] (no subject) > > Ah, ok. I remember. You are getting an access violation because the > thread that runs the load command cannot also run the JavaScript command. > > Problem: I want to load a file using the dialog in the signed applet and > then after that run some JavaScript. > > Solution: You must use the message callback mechanism to let your page know > that the loading is done, and from THAT function, run your JavaScript: > > > function loadModels(){ > removeAllModels() > var Info = jmolGetPropertyAsArray("auxiliaryInfo.models") > .. etc... > } > > function myMessageCallback(a,m) { > m = "" + m > // important to do this to change from Java string to JavaScript string > if (m.indexOf("DONE") == 0) loadModels() > } > > function onClickLoadStruc() { > jmolScript("load ?; background white;set messageCallback > 'myMessageCallback';message DONE") > } > > > > > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 [Jmol-users] (no subject) From: P.Canepa - 2010-07-20 15:01:24 Thanks Jonathan I got your script and I was trying to use it. My HTML page has the script set like that The array Colorscript should be the array which include the name of the function to call, see below the function setAtomColor() is written as : var atomColor = ""; function elementSelected(element){ setValue("select none; halo off; label off"); setValue("select " + element + "; halo on; label on"); atomColor = "' color " + element; return atomColor; } function setAtomColor (rgbCodeStr, Colorscript , jmolApplet0, atomColor){ var finalColor = " " + atomColor + " " + rgbCodeStr + " "; return finalColor; } I think I got your explanation wrong in the headings of your script. Is the rgbCodeStr the color selected by jmolColorPickerBox ? Thanks a lot, Piero -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- 
 [Jmol-users] (no subject) From: - 2010-10-07 16:23:20 Attachments: Message as HTML Hi, i am trying to implement in my blog (http://pinostriccoli.altervista.org) JME TO JMOL (or JChempaint as in http://biomodel.uah.es/en/DIY/JChemPaint3/draw.en.htm), so that the two applets will be displayed in just one window. At the moment there is a link to Molinspiration that i would like to change.Where can i download the files ? ThanksPino 
 Re: [Jmol-users] (no subject) From: Angel Herráez - 2010-10-07 20:00:37 > i am trying to implement in my blog (http://pinostriccoli.altervista.org) JME TO JMOL (or > JChempaint as in http://biomodel.uah.es/en/DIY/JChemPaint3/draw.en.htm), so that the two > applets will be displayed in just one window. > At the moment there is a link to Molinspiration that i would like to change.Where can i download > the files ? Which files, Pino? JME? http://www.molinspiration.com/jme/index.html points you to "How to get JME" http://www.molinspiration.com/jme/getjme.html which says "The latest version of JME editor applet may be obtained for non-commercial use directly from its author Peter Ertl [...] To request JME send an email ..." 
 Re: [Jmol-users] (no subject) From: Angel Herráez - 2010-10-07 22:08:38 > I already have JME working in my page on my weblog, Actually i can see > the molecule in 3d on molinspiration.com. I would like to use just Jmol > in the same page with JME or Jchempaint. > What do I need to display the two applets working and connected on the > same page ? Jmol will accept either the JME string or a MOL exported from JME. You can extract the JME into a javascript variable, then use that to fill Jmol applet using JmolLoadInline() Check the source of my page http://biomodel.uah.es/en/DIY/JME/JME.htm or Bob's page that does the same http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm I'm not sure however about how all this can be fit into the blog. Have you read the Jmol Wiki section about implementing Jmol in blogs? 
 Re: [Jmol-users] (no subject) From: Mio_libero - 2010-10-08 09:31:10  Thanks Angel, i will read wiki about this and adapt the code to my case. I think it will be a bit difficult with blog but i already did something in my blog, so i hope i can succed. Pino Il 08/10/2010 0.15, Angel Herráez ha scritto: >> I already have JME working in my page on my weblog, Actually i can see >> the molecule in 3d on molinspiration.com. I would like to use just Jmol >> in the same page with JME or Jchempaint. >> What do I need to display the two applets working and connected on the >> same page ? > Jmol will accept either the JME string or a MOL exported from JME. You can extract the JME > into a javascript variable, then use that to fill Jmol applet using JmolLoadInline() > Check the source of my page http://biomodel.uah.es/en/DIY/JME/JME.htm > or Bob's page that does the same > http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm > > I'm not sure however about how all this can be fit into the blog. Have you read the Jmol Wiki > section about implementing Jmol in blogs? > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 Re: [Jmol-users] (no subject) From: Mio_libero - 2010-10-08 10:43:32  One more think, Angel. I tried JME, Jpaintdraw with PCl5 molecule. The Jmol optimization is not trigonal bipyramidal as expected. Am i wrong or is it an issue in JMOL? Pino >> I already have JME working in my page on my weblog, Actually i can see >> the molecule in 3d on molinspiration.com. I would like to use just Jmol >> in the same page with JME or Jchempaint. >> What do I need to display the two applets working and connected on the >> same page ? > Jmol will accept either the JME string or a MOL exported from JME. You can extract the JME > into a javascript variable, then use that to fill Jmol applet using JmolLoadInline() > Check the source of my page http://biomodel.uah.es/en/DIY/JME/JME.htm > or Bob's page that does the same > http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm > > I'm not sure however about how all this can be fit into the blog. Have you read the Jmol Wiki > section about implementing Jmol in blogs? > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 [Jmol-users] JME From: Mio_libero - 2010-10-12 18:15:28  Angel, I downloaded your page "testingJME" on my website http://singa.altervista.org/chimica/JME.htm When i try to transfer the structure to Jmol, nothing happens and firefox gives me an error Errore: jmolLoadInlineScript is not defined File sorgente: http://singa.altervista.org/chimica/JME.htm Riga: 1 What has gone wrong? I hope that the download (at the moment for trial only) is allowed. If all goes ok there will be of course the credit and link to original pages or to anywhere you say Pino 
 Re: [Jmol-users] JME From: Angel Herráez - 2010-10-12 18:35:52 Hello Pino On 12 Oct 2010 at 20:15, Mio_libero wrote: > When i try to transfer the structure to Jmol, nothing happens and > firefox gives me an error > > Errore: jmolLoadInlineScript is not defined > What has gone wrong? That sounds like you don't have Jmol.js accesible. Check your files and paths. Do you see the Jmol applet? > I hope that the download (at the moment for trial only) is allowed. If > all goes ok there will be of course the credit and link to original > pages or to anywhere you say It's OK. My DIY pages are under Creative Commons by-nc-sa so you should adhere explicitly to that. > Pino > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 Re: [Jmol-users] JME From: Angel Herráez - 2010-10-12 19:23:25 You need to have all the jmolApplet0*.jar files available for the page. The error I'm getting in your page is not what you mention, but this: File reader was not found:Mol which suggests that some of the applet files are not available Also, the Jmol applet popup menu is not opening. 
 Re: [Jmol-users] JME From: Mio_libero - 2010-10-12 20:20:49  Yes true. This error i found after fixing the path. is it as if it can read the molfile? Pino > You need to have all the jmolApplet0*.jar files available for the page. > > The error I'm getting in your page is not what you mention, but this: > File reader was not found:Mol > which suggests that some of the applet files are not available > > Also, the Jmol applet popup menu is not opening. > > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 Re: [Jmol-users] JME From: Angel Herráez - 2010-10-12 22:09:57 On 12 Oct 2010 at 22:21, Mio_libero wrote: > Yes true. This error i found after fixing the path. is it as if it can > read the molfile? I would say that it is not finding some of the needed jmolApplet0*.jar files Make sure you have all files from the Jmol zip distribution present in the folder. 
 Re: [Jmol-users] JME From: Mio_libero - 2010-10-13 08:56:05  Hi Angel, i put all the files in the directory so now it is working. Next move it is to implement it in wordpress. Thanks Pino > On 12 Oct 2010 at 22:21, Mio_libero wrote: > >> Yes true. This error i found after fixing the path. is it as if it can >> read the molfile? > I would say that it is not finding some of the needed jmolApplet0*.jar files > Make sure you have all files from the Jmol zip distribution present in the folder. > > > > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 [Jmol-users] JME e Jmol in wordpress From: Mio_libero - 2010-10-14 17:58:47  Hi, i forgot to tell that i had to use the tag to insert Jmol. WIth the Javascript code it doesn't work, giving always the error JmolAplet.class not found. Maybe it cannot find Jmol.js? Pino 
 Re: [Jmol-users] JME e Jmol in wordpress From: Angel Herráez - 2010-10-14 19:50:09 > Hi, i forgot to tell that i had to use the tag to insert > Jmol. WIth the Javascript code it doesn't work, giving always the error > JmolAplet.class not found. Maybe it cannot find Jmol.js? Usually, when Jmol.js is not found the error is "jmolInitialize() is not defined" The potential problem with using the APPLET tag directly is browser compatibility. That's one of the issues that Jmol.js takes care of. Have you read Henry Rzepa's notes about using Jmol in WordPress? He mentions the need to insert the call to Jmol.js into the style header. 
 [Jmol-users] (no subject) From: pieremanuele canepa - 2010-11-11 16:44:34 Attachments: Message as HTML Dear All, Can you show me the Jmol command to add a new atom knowing its fractional or Cartesian coordinates? Thanks a lot, Piero -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229@... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- 
 [Jmol-users] (no subject) From: - 2012-09-21 12:25:26 Attachments: Message as HTML Hi everybody. I have a simple issue. A mistake in rendering cicloexane ring from JME to Jmol. At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure the error. I remember being an old issue with Jmol. It appears in Jmol13, and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr ring for cycloexane. What happens ?Pino 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2012-09-21 13:40:53 Attachments: Message as HTML It works at http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htm without a problem. I'll take a look at your page to see what is going on there. On Fri, Sep 21, 2012 at 7:25 AM, pino.striccoli@... < pino.striccoli@...> wrote: > Hi everybody. I have a simple issue. A mistake in rendering cicloexane > ring from JME to Jmol. > > At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure > the error. I remember being an old issue with Jmol. It appears in Jmol13, > and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr > ring for cycloexane. What happens ? > > Pino > > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2012-09-21 13:45:00 Attachments: Message as HTML try using the JME output rather than the MOL file output. On Fri, Sep 21, 2012 at 8:40 AM, Robert Hanson wrote: > It works at > http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htmwithout a problem. I'll take a look at your page to see what is going on > there. > > On Fri, Sep 21, 2012 at 7:25 AM, pino.striccoli@... < > pino.striccoli@...> wrote: > >> Hi everybody. I have a simple issue. A mistake in rendering cicloexane >> ring from JME to Jmol. >> >> At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure >> the error. I remember being an old issue with Jmol. It appears in Jmol13, >> and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr >> ring for cycloexane. What happens ? >> >> Pino >> >> >> >> ------------------------------------------------------------------------------ >> Got visibility? >> Most devs has no idea what their production app looks like. >> Find out how fast your code is with AppDynamics Lite. >> http://ad.doubleclick.net/clk;262219671;13503038;y? >> http://info.appdynamics.com/FreeJavaPerformanceDownload.html >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2012-09-21 13:51:16 Attachments: Message as HTML This worked: jmolLoadInlineScript( gid('editor').jmeFile(),"") On Fri, Sep 21, 2012 at 8:40 AM, Robert Hanson wrote: > It works at > http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolSmilesTest.htmwithout a problem. I'll take a look at your page to see what is going on > there. > > On Fri, Sep 21, 2012 at 7:25 AM, pino.striccoli@... < > pino.striccoli@...> wrote: > >> Hi everybody. I have a simple issue. A mistake in rendering cicloexane >> ring from JME to Jmol. >> >> At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure >> the error. I remember being an old issue with Jmol. It appears in Jmol13, >> and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr >> ring for cycloexane. What happens ? >> >> Pino >> >> >> >> ------------------------------------------------------------------------------ >> Got visibility? >> Most devs has no idea what their production app looks like. >> Find out how fast your code is with AppDynamics Lite. >> http://ad.doubleclick.net/clk;262219671;13503038;y? >> http://info.appdynamics.com/FreeJavaPerformanceDownload.html >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Chemistry Department > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2012-09-21 13:42:08 Attachments: Message as HTML Oh, one thing I see is that you are using an older JME applet. Try the one in http://chemapps.stolaf.edu/jmol/docs/examples-12 Although I don't think that is the problem. On Fri, Sep 21, 2012 at 7:25 AM, pino.striccoli@... < pino.striccoli@...> wrote: > Hi everybody. I have a simple issue. A mistake in rendering cicloexane > ring from JME to Jmol. > > At my page http://pinostriccoli.altervista.org/?page_id=873, it is sure > the error. I remember being an old issue with Jmol. It appears in Jmol13, > and i checked again on http://biomodel.uah.es/en/DIY/JME/JME.htm. Palanr > ring for cycloexane. What happens ? > > Pino > > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Angel Herráez - 2012-09-21 15:21:00 Hi Pino Yes, this problem has been there always with reading MOLfile data. As Bob says, using the JME format for the transfer fixes it. You can see both demonstrated in my page (compare the 2 buttons) http://biomodel.uah.es/en/DIY/JME/JME.htm If you still need to use MOL (as I do in my pages that do not use JME but other editors), the problem only affects a few very symmetrical molecules like cyclohexane and tert-butane. I just had the idea of changing the Z coord of one of the atoms (to break the symmetry) and it works for cyclohexane, see http://biomodel.uah.es/en/DIY/JME/JME2.htm but not for tert-butane as Jmol wrongly interprets tertiary carbons as planar (there was discussion about this some time ago and I guess some conclusion that I cannot remember, but I could not find a solution to apply to my page --but this is another issue.) PS: Could you please ammend my name in your page? Thanks 
 [Jmol-users] Display only a single protein chain From: Andreas Truszkowski - 2012-09-25 13:04:02 Hi, I can't find any script snippets on how to display only a single chain of an entire protein. E.g. Insulin (PDB: 4INS) has two compounds with each having 2 chains. How can I hide/display the chains independently. Kind regards, Andreas 
 Re: [Jmol-users] Display only a single protein chain From: Angel Herráez - 2012-09-25 13:18:52 Hi Andreas You need to find out the chain IDs (usually A, B ... but not always) Then display *:A; // will also hide all the others display add *:A; // makes A visible without hiding others etc. Check the DISPLAY and HIDE commands in the documentation 
 Re: [Jmol-users] Display only a single protein chain From: Andreas Truszkowski - 2012-09-25 13:29:41 Thank you very much. But hiding/displaying of protein chains is not documented. Kind regards, Andreas Am 25.09.2012 15:18, schrieb Angel Herráez: > Hi Andreas > > You need to find out the chain IDs (usually A, B ... but not always) > Then > > display *:A; // will also hide all the others > display add *:A; // makes A visible without hiding others > > etc. > Check the DISPLAY and HIDE commands in the documentation > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > 
 Re: [Jmol-users] Display only a single protein chain From: Angel Herráez - 2012-09-25 13:35:38 Sorry, hiding and displaying of ANYTHING is documented. You just combine display command with atom expressions, which are described in the doc (and used by most commands). Good luck! 
 [Jmol-users] ion sizes From: Pshemak Maslak - 2012-09-25 13:46:36 Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of Cl-. I am assuming that atomic radii are use. Is there ionic radii info in Jmol? If so, how can one display it? PM 
 Re: [Jmol-users] ion sizes From: Otis Rothenberger - 2012-09-25 14:29:38 I'm playing with CIF files for the first time myself. The radii are VdW, and the following script components may be useful to you: connect delete;spacefill IONIC 30%;label "" Edit features in or out per your needs. Otis -- Otis Rothenberger otis@... http://chemagic.com On Sep 25, 2012, at 9:46 AM, Pshemak Maslak wrote: > Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of > Cl-. I am assuming that atomic radii are use. Is there ionic radii info > in Jmol? If so, how can one display it? > > PM > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 Re: [Jmol-users] ion sizes From: Phillip Barak - 2012-09-25 14:06:58 spacefill ionic --pb On 09/25/12, Pshemak Maslak wrote: > Displaying NaCl (from a cif file) shows Na+ sphere bigger than that of > Cl-. I am assuming that atomic radii are use. Is there ionic radii info > in Jmol? If so, how can one display it? > > PM > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 [Jmol-users] (no subject) From: - 2013-08-27 16:56:53 Attachments: Message as HTML After a long break from JSmol, i decided to upload the last version of JSmol and continue working on my pages, but i found some problems with these pages http://pinostriccoli.altervista.org/html5/index.htmlwhen trying to load molecoles in pdb. It seems loading just mol and xyz files.I have the error file reader not found .... Any suggestion?did i do some mistake in uploading? Thanks a lotPino 
 Re: [Jmol-users] (no subject) From: Rolf Huehne - 2013-08-27 17:21:54 On 08/27/2013 06:56 PM, pino.striccoli@... wrote: > After a long break from JSmol, i decided to upload the last version of JSmol and continue working on my pages, but i found some problems with these pages http://pinostriccoli.altervista.org/html5/index.htmlwhen trying to load molecoles in pdb. It seems loading just mol and xyz files.I have the error file reader not found .... Any suggestion?did i do some mistake in uploading? > Thanks a lotPino > Your update didn't work correctly. The JSmol version that is shown in the JSmol menu on your page is '13.1.12_dev' but the latest is at least 13.3.4. You should try updating again. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhuehne@... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 
 Re: [Jmol-users] (no subject) From: Angel Herráez - 2013-08-27 17:26:08 Hello Pino I looked at your source code. Some things have changed, particularly integration with jQuery (and that deals with the AJAX methods for loading files from remote servers, as fas as I understand). Instead of calling several JS files, you should just call jsmol.min.js See the Wiki > JSmol page for more details 
 [Jmol-users] (no subject) From: - 2013-09-16 21:13:00 Hi Friends, i am trying to format the page http://pinostriccoli.altervista.org/? p=6434 and i want the molecule floating to the left so that written text gos to its right. I found jmol.setAppletCss. Where should I insert the script and what can be the exat sintax? thanks Pino 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2013-09-16 22:40:12 Attachments: Message as HTML The jQuery way to do that would be somethng like this: $("#jmolApplet0_appletinfotablediv").css({top:"5px",left:"400px"}) where "jmolApplet0" is the name of my applet. Bob On Mon, Sep 16, 2013 at 4:12 PM, pino.striccoli@... < pino.striccoli@...> wrote: > Hi Friends, i am trying to format the page > http://pinostriccoli.altervista.org/? > p=6434 > and i want the molecule floating to the left so that written text gos to > its > right. > I found jmol.setAppletCss. Where should I insert the script and what can be > the exat sintax? > thanks > Pino > > > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just$49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, > SharePoint > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack > includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Angel Herráez - 2013-09-17 07:43:08 Ciao Pino http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Functions_that_s et_CSS_rules explains it. > I found jmol.setAppletCss. Where should I insert the script and what can be > the exat sintax? Not exact, but something like this: Before the call to getJmolApplet: Jmol.setAppletCss(".toLeft") as long as you have defined the css code for class "toLeft" or Jmol.setAppletCss("style='float:left'") 
 [Jmol-users] (no subject) From: Carl McBride - 2013-11-14 11:18:50  This is not really a bug, I am just looking for an idiots guide to running both JSmol (jmol-13.2.8) in conjunction with MathJax (release branch v2.2) on a MediaWiki (1.21.2) site without getting a red [Math Processing Error]. All the best, carl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dr. Carl McBride Departamento de Ciencias y Técnicas Fisicoquímicas Facultad de Ciencias Universidad Nacional de Educación a Distancia (UNED) 28040 Madrid Spain friedel.uned.es/carlmcbride.html http://www.SklogWiki.org >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2013-11-14 18:42:03 Attachments: Message as HTML Do we have that on the wiki yet, Angel? If not, we need to add it. Since MathJax actually rewrites the entire page after loading, you have to make sure your Jmol applet is added within a script that runs only after MathJax is complete. Not sure if MathJax has a callback on that, but there is a div on the page that is hidden and is reporting MathJax progress. Here is a rendition of that prior message on this list, updated a bit for newer JSmol.min.js versions. It's a pretty simple solution. Really what the problem is is that both Jmol and MathJax are competing for the AJAX processing. For compatibility with MathJax, make sure: 1) you are using dynamic loading of the applet -- no
 Re: [Jmol-users] (no subject) From: Angel Herráez - 2013-11-14 19:05:55 No, we don't have it in the Wiki. I remember some former thread about MathJax but did not take note. I will try to do it some day I think there is a page on compatibility with other frameworks/libraries, it could go there 
 [Jmol-users] (no subject) From: - 2013-11-26 17:14:29 Can anybody explain to me this error i find on this page http://pinostriccoli. altervista.org/?p=5589? On firefox (windows or linux) it works ok. In Chrome (windows or Linux) gives me unrecognised format error. What happens? any idea? Pino 
 Re: [Jmol-users] (no subject) From: Jaime Prilusky - 2013-11-26 17:54:51 Chrome 31.0.1650.57 and Safari Version 7.0 (9537.71) on Mac 10.9 also gave format error, most probably the same you got. Simply Javascript on Firefox (Gecko engine) runs under different rules than on Chrome/Safari (WebKit engine). Jaim On Nov 26, 2013, at 7:14 PM, pino.striccoli@... wrote: > Can anybody explain to me this error i find on this page http://pinostriccoli. > altervista.org/?p=5589? > On firefox (windows or linux) it works ok. In Chrome (windows or Linux) gives > me unrecognised format error. > What happens? any idea? > Pino > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users 
 [Jmol-users] (no subject) From: - 2014-01-24 16:17:32 carlon@... 
 [Jmol-users] (no subject) From: Ron Mignery - 2014-01-25 04:18:27 Attachments: Message as HTML I use the application, not the applet. Can I use the javascipt command there? The documentation describes the javascript command as applet only. On Fri, 24 Jan 2014 at 5:08 PM, Robert Hanson wrote >I would just use the javascript command to introduce your own audio >components. >On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery wrote: >> Could a play command similar to the Java play function be >> added to scripting? This would allow clicks and beeps or even entire >> narrations to be added to Jmol animations. Hopefully it would run in a >> separate thread. 
 Re: [Jmol-users] (no subject) From: Robert Hanson - 2014-01-25 04:35:36 Attachments: Message as HTML I don't see the Jmol application as much more than a development tool. The target environment for Jmol is a web page. On Fri, Jan 24, 2014 at 11:18 PM, Ron Mignery wrote: > I use the application, not the applet. Can I use the javascipt command > there? The documentation describes the javascript command as applet only. > > On Fri, 24 Jan 2014 at 5:08 PM, Robert Hanson wrote > > >I would just use the javascript command to introduce your own audio > >components. > > > >On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery wrote: > > >> Could a play command similar to the Java play function be > >> added to scripting? This would allow clicks and beeps or even entire > >> narrations to be added to Jmol animations. Hopefully it would run in a > >> separate thread. > > > ------------------------------------------------------------------------------ > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
 Re: [Jmol-users] (no subject) From: Angel Herráez - 2014-01-25 12:33:17 Ron, the question is: who would run the Javascript? There is no JS interpreter if you are not in a webpage `