From: Patrick J. C. <ca...@do...> - 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? |
From: Michael T H. <mth...@mt...> - 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? -------------------------------------------------- |
From: Michael T H. <mth...@mt...> - 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" <mth...@mt...> > To: <Jmo...@li...> > 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 >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users -------------------------------------------------- Miguel Howard mi...@ho... 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 -------------------------------------------------- |
From: <chr...@ph...> - 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 |
From: Miguel H. <mi...@ho...> - 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 |
From: Miguel <mt...@mt...> - 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 |
From: Sriram R. <ramarat@CLEMSON.EDU> - 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 |
From: Bob H. <ha...@st...> - 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 <param name="script" value="load Fischer_Files/R.pdb; spin on; wireframe 0.15; select all; cpk 0.5;select Bromine, Chlorine, Fluorine; label %e;"> 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 > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |
From: Miguel <mi...@jm...> - 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 |
From: Nick G. <ngr...@li...> - 2005-04-19 14:06:11
|
> From: Bob Hanson <ha...@st...> > To: jmo...@li... > Subject: [Jmol-users] power of jmol applet > Reply-To: jmo...@li... > > 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) |
From: J. D. P. <pol...@os...> - 2005-08-27 14:58:24
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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 |
From: Egon W. <e.w...@sc...> - 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/ |
From: Muriel C. <mur...@eb...> - 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 |
From: Miguel <mi...@jm...> - 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 |
From: David L. <d.l...@bi...> - 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 _______________________________________________________________ |
From: Miguel <mi...@jm...> - 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 |
From: Aaron G. <ag...@ca...> - 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 |
From: Miguel <mi...@jm...> - 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 |
From: Aaron G. <ag...@ca...> - 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 > Jch...@li... > https://lists.sourceforge.net/lists/listinfo/jchempaint-user > |
From: jeff g. <je...@ya...> - 2006-01-07 01:33:29
|
Hey guys, I'm trying to check out the Jmol project, but I think the sourceforge server is on the fritz: cvs -d:pserver:ano...@cv...:/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. |
From: Egon W. <e.w...@sc...> - 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:ano...@cv...:/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.w...@sc... 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 |
From: Miguel <mi...@jm...> - 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 |
From: ranjan s. <ran...@gm...> - 2006-07-07 06:52:20
|
From: Craig T M. <cm...@ch...> - 2006-09-29 14:47:47
|
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 <rh...@fl...> > Subject: [Jmol-users] Saving image with applet - possible solution > Message-ID: <451...@fl...> > > 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 cm...@ch... |
From: Frieda R. <fr...@ns...> - 2007-03-01 03:10:05
|
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 /////////////////////////////////////////// |