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From: Alan H. <he...@il...> - 2006-08-24 12:22:43
|
<html> <body> Thanks Bob.<br> For the moment I have implemented the 1st solution of uploading the file to my server, though I am nervous about the security aspects of that. This can be tried on <a href="http://icsd.ill.fr/icsd/help/CIF-help.html" eudora="autourl"> http://icsd.ill.fr/icsd/help/CIF-help.html</a> by displaying the demo Y1Ba2Cu3O7 structure and then using the controls at the bottom of the resulting structure display to browse and upload a local file. My Jmol script works for CIF and ShelX files, but not for PDB and some others. <br> <b>Question: </b>Why doesn't it display PDB, simply ignoring any script commands that are not appropriate?<br> Keeping a copy on my server allows it to be reloaded with different parameters, so I would like to find a way of improving the security of doing that. But I could reload in line I guess.<br> <b>Question:</b> How does Jmol report success or failure in displaying a file ? If I could determine that, I could simply delete suspicious files that did not display immediately.<br> But I will look further at the "loadinline" suggestion.<br><br> <blockquote type=cite class=cite cite="">The business of the ######### is that certain CIF files from a<br> certain database can't be read directly (right now) because they have too<br> many bytes of comment at the top.</blockquote><br> You mean from ICSD ? Yes I have rather large comments with ##### but these CIF files work with my own Jmol script. I could reduce those comments if that is a problem - they are only generated on the fly.<br><br> Many thanks again, Alan.<br><br> At 23:27 23/08/2006, Bob wrote:<br> <blockquote type=cite class=cite cite="">> What is the easiest way of loading a local file using a remote server ?<br><br> No easy solution. Java security precludes reading a file from the user's<br> system directly. Two options I know of:<br><br> 1) mirror it from your server:<br><br> a) Have a form with <input type=text> with which the user can designate a<br> local file.<br> b) Have a server-side script that returns that text embedded in an applet<br> tag as part of a "loadInline" parameter. This removes the need to save the<br> file in any temporary way on your server. The trick here is that you need<br> to add a vertical line at the beginning of each line, because HTML will<br> strip lines from a parameter.<br><br> 2) have the user clip the data into a text area. The code used at XTALX<br> uses this method. It is simpler, but it asks more of your user.</blockquote><br><br> </body> <br> <div>_____________________________________________________________</div> <div>Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48</div> <div>+33.476.20.72.13 (.26 Mme Guillermet) <a href="http://www.ill.fr/dif/AlanHewat.htm" EUDORA=AUTOURL> http://www.ill.fr/dif/AlanHewat.htm</a> </div> <div>_____________________________________________________________</div> </html> |
From: <ha...@st...> - 2006-08-24 06:54:20
|
The dots not changing color is certainly a bug that will be fixed in 10.9.47 (later today). As for the action of restrict, this is intentional. (That is, a feature, not a bug.) Let's discuss what we really mean by dots. Here's the deal: Note that dots do not simply surround an atom. They take into account neighboring atoms. Thus, unlike spacefill, dots are not just "displayed", they are the result of a rather complex calculation -- essentially the solvent-accessible-surface calculation. (They are not quite the solvent-accessible surface, because they do not take into account all the other atoms around the selected set. "isosurface sasurface" takes this into account, but "dots" does not. In fact, "select *;dots +1.2" IS the solvent-accessible surface.) (Oh, I do so hate "restrict"!) I'll look into whether restrict could properly restrict to part of the dot surface, but the thinking on the part of Miguel and me up until now is that since dots depend upon neighbors, and restrict changes neighborhoods, dots should be completely removed if a restrict command is given. The basic problem is that the following two will be different (which might be OK): select *; dots on; restrict (atomno < 10); # this would be a partial surface, like the action of sasurface? restrict (atomno < 10); dots on; # this would be a continous surface around those atoms. Bob > First, any restrict command (including "restrict not none" and "restrict > all", which do not affect any renderings that I know of except dots) hides > ALL dots. It seems to me that using "restrict" to hide a subset of atoms > should not hide ALL dots -- it should hide dots only for the set hidden -- > just as it does for spacefill, etc. > > Second, "dots off" hides ALL dots, even when preceded with "select none". > > Working around these bugs in FirstGlance in Jmol has required adding a lot > of messy javascript. It would be great to have them fixed! > > Thanks, -Eric > > > ---- > Eric Martz, Professor Emeritus, Dept Microbiology > University of Massachusetts, Amherst MA US > http://www.umass.edu/molvis/martz > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: Eric M. <em...@mi...> - 2006-08-24 00:19:13
|
Yes, I agree, David. I love the way Jmol automatically adjusts dot density with zoom -- Chime did not do this and it was a problem. But I agree that when the molecule is zoomed to small size (or with a very large molecule so the atoms must be small to fit the molecule in the view space), the dots density is too low, and it is hard to see the dots. So I would also like an option to at least increase dot density when currently the density is too low to see well. It is possible this could also be solved without any option -- just by making the dot density higher when the atoms are small. -Eric At 8/23/06, you wrote: >One nice feature of Chime/RasMol was the ability to change the density >of dots. This was very useful when zooming in to show, for example, >interacting protein side chains. > >In Jmol, with the current dots option (fixed density), it is difficult >to see the dots at high levels of zoom. > >Are there others who would like to see a variable dots density option? >If so, would there be a way to fit this in with the development team's >plans for future releases? > >Just a suggestion. > >Cheers, >David > >-- ><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> >David Marcey >Fletcher Jones Professor of Developmental Biology >Chair, CLU Biology Department >60 W. Olsen Rd., MC3700 >Thousand Oaks, CA 91360 >(805)-493-3263, 3590 >ma...@cl... ><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> > > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ |
From: Eric M. <em...@mi...> - 2006-08-23 19:06:41
|
There appear to me to be bugs that hide dots inappropriately with "restrict" and "dots off" commands. These bugs are present in 10.2.0 and 10.x.46d. If those in the know agree that these are bugs, I'll submit this as a bug fix request. Jmol, to its credit and unlike Chime, can add dots to newly selected atoms after some dots are already displayed, and even color them differently. For example, for 1d66, in 10.2.0, restrict none select :a dots color dots green # now there are green dots for chain A select :b dots # now CPK-colored dots have been added for chain B There appear to me to be two bugs in both versions. [In 10.x.46d there is a new bug: "color dots green" no longer works.] First, any restrict command (including "restrict not none" and "restrict all", which do not affect any renderings that I know of except dots) hides ALL dots. It seems to me that using "restrict" to hide a subset of atoms should not hide ALL dots -- it should hide dots only for the set hidden -- just as it does for spacefill, etc. Second, "dots off" hides ALL dots, even when preceded with "select none". Working around these bugs in FirstGlance in Jmol has required adding a lot of messy javascript. It would be great to have them fixed! Thanks, -Eric ---- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz |
From: David M. <ma...@cl...> - 2006-08-23 09:25:47
|
One nice feature of Chime/RasMol was the ability to change the density of dots. This was very useful when zooming in to show, for example, interacting protein side chains. In Jmol, with the current dots option (fixed density), it is difficult to see the dots at high levels of zoom. Are there others who would like to see a variable dots density option? If so, would there be a way to fit this in with the development team's plans for future releases? Just a suggestion. Cheers, David -- <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> David Marcey Fletcher Jones Professor of Developmental Biology Chair, CLU Biology Department 60 W. Olsen Rd., MC3700 Thousand Oaks, CA 91360 (805)-493-3263, 3590 ma...@cl... <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> |
From: <ha...@st...> - 2006-08-22 22:28:55
|
Assadullah, The problem is two-fold. First, we haven't set up Jmol for reading the symmetry information in CML files. This is primarily because no one has asked until now. Be aware that some of your files are invalid because they contain < instead of "<". For example: http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/crystal1.html <cml title="crystal example"> <molecule id="m1"> But some of the others are OK. Please enter this as a feature request at http://sourceforge.net/tracker/?func=add&group_id=23629&atid=379136 Bob Hanson > Greetings: > > I tried to load the sample crystals listed at > http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/ > including > CRYSTAL1.XML, crystal1.html, and > crystal2.html. jmol loaded the latter two fine, but > did not display the crystals. > > I am wondering if I need to add addtional markup than > what is in the sample files or if I need to configure > jmol properly. > > Regards, > > Assadullah > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: <ha...@st...> - 2006-08-22 21:52:06
|
> > What is the easiest way of loading a local file using a remote server ? No easy solution. Java security precludes reading a file from the user's system directly. Two options I know of: 1) mirror it from your server: a) Have a form with <input type=text> with which the user can designate a local file. b) Have a server-side script that returns that text embedded in an applet tag as part of a "loadInline" parameter. This removes the need to save the file in any temporary way on your server. The trick here is that you need to add a vertical line at the beginning of each line, because HTML will strip lines from a parameter. 2) have the user clip the data into a text area. The code used at XTALX uses this method. It is simpler, but it asks more of your user. The code XTALX uses is: function doloadcifdata() { var s=document.getElementById("cifdata").value.replace(/\n\ /g,"\n") if(s.indexOf("########################################################################################")>0) { var i = s.lastIndexOf("########################################################################################") s=s.substring(i,s.length) } jmolScriptWait(getlatticeinfo("set defaultlattice ")) lastinlineload=s jmolLoadInlineScript(s,loadscript) } Here "cifdata" is the ID of the textarea. That first replace isn't necessary. The business of the ######### is that certain CIF files from a certain database can't be read directly (right now) because they have too many bytes of comment at the top. You could probably dispense with that as well. The jmolScriptWait command simply reads the current lattice info (from another function) and then finally loads the script. The following will probably work just fine for you: jmolLoadInlineScript(document.getElementById("cifdata")) where we have <textarea wrap=OFF id=cifdata rows=8 cols=50> </textarea> on the page somewhere. So this method asks a bit more of the user but is far easier to implement. Bob |
From: Alan H. <he...@il...> - 2006-08-22 15:48:14
|
Alan Hewat wrote: http://icsd.ill.fr/icsd/index.php?action=Search&elements=na8+si7+o18 This doesn't give any result for most users. I should have written eg: http://icsd.ill.fr/icsd/index.php?action=Search&elements=na2+si2+o5 Alan. _____________________________________________________________ Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm _____________________________________________________________ |
From: Alan H. <he...@il...> - 2006-08-22 15:30:30
|
I have found time to make use of Bob's latest 11-beta features for selecting atom sites and creating new polyhedra/bonds eg click on the formula found with the following search, then check "Select" and click on the two different (blue) sodium sites, then check "Create": http://icsd.ill.fr/icsd/index.php?action=Search&elements=na8+si7+o18 I'm still learning how to best use these great new features, but already I have another question :-) What is the easiest way of loading a local file using a remote server ? I would like to add a "Load" button to allow the user to visualise his own files using my interface, not just those generated by the remote ICSD server. My first thought was to open a file dialogue, allow the user to select his local file, upload it to the server and display it. But then I found Bob's XTALX (Jmol Crystal Explorer) on http://fusion.stolaf.edu/chemistry/jmol/xtalx/ where the user can simply load the contents of a text window. It is so fast that I suppose it isn't first uploaded to his server, but since this page also does lots of other things and uses various javascript file collections on Bob's server, I couldn't easily work out how it was being done. Alan. _____________________________________________________________ Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm _____________________________________________________________ |
From: Egon W. <ewi...@un...> - 2006-08-22 13:38:33
|
Hi all, Bob and I have just renamed Bob's private development branch for the 10.x.46 (etc) series in SVN. It was previously available as jmol/branches/bob200603, and is now available as jmol/branches/v10_9. So, the next release in his series will be called 10.9.47. The 9 indicates a development release, so the first stable release from this branch will be called 11.0. Minor releases after that would be called 11.0.x, and the next major stable release (depending on the amount of changes) would be either 11.2 or 12.0. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: Mir M. A. <ass...@ya...> - 2006-08-22 13:32:45
|
Greetings: > Jmol might not be happy about the namespace prefix yet, but will need > to > verify that tomorrow. It complains when I run it on Windows XP and doesn't complain when I run it on Red Hat. > A question: does it show no atoms at all? If it would one Na and one Cl > then > that would be expected, because Jmol does not 'do' the symmetry yet. No atoms appear, I don't see any errors on the console on linux either. Does jmol not do symmetry for CML or does it not do for any of the formats? Do you happen to know of any (preferably free) software that I can use to convert CML to expanded and symmetrized XYZ or CML format so that I can use jmol to display the molecule on the web in an applet? Regards, Assadullah __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
From: <ha...@st...> - 2006-08-22 08:00:19
|
> Thanks, Bob, for your amazingly quick response and fix of the refresh bug. > > Now, I've encountered a second changed behavior of the newer versions > compared to 10.2 with respect to "labeloffset." In 10.2, one could, > very conveniently, select an atom, label it, and offset the label to a > specified coordinate independent of other labels on other atoms that > might be offset to different relative positions vis a vis their selected > atoms. In post-10.2 versions, it seems that the last labeloffset governs > all labels that had been previously assigned. Is there any way to > restore the labeloffset independence of 10.2 in 11-beta? David, I appreciate your giving this a workout. Keep it coming! Another easy fix. A new Jmol-11-beta.zip is being uploaded at this moment. (Give it a few minutes to complete, please). 10.x.46d in http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11 Bob > > Thanks for considering this. > > David > > ha...@st... wrote: > >>Thanks very much for spotting that, David. This was an easy fix. >> >>10.x.46c >> >>See Jmol-11-beta.zip 21-Aug-2006 19:46 and associated files in >> >> http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11 >> >>For the record, it was a failure of Jmol to do a (newly required) >>"refresh" before the move or moveto command. >> >> >> > > -- > <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> > David Marcey > Fletcher Jones Professor of Developmental Biology > Chair, CLU Biology Department > 60 W. Olsen Rd., MC3700 > Thousand Oaks, CA 91360 > (805)-493-3263, 3590 > ma...@cl... > <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: David M. <ma...@cl...> - 2006-08-22 04:08:29
|
Thanks, Bob, for your amazingly quick response and fix of the refresh bug. Now, I've encountered a second changed behavior of the newer versions compared to 10.2 with respect to "labeloffset." In 10.2, one could, very conveniently, select an atom, label it, and offset the label to a specified coordinate independent of other labels on other atoms that might be offset to different relative positions vis a vis their selected atoms. In post-10.2 versions, it seems that the last labeloffset governs all labels that had been previously assigned. Is there any way to restore the labeloffset independence of 10.2 in 11-beta? Thanks for considering this. David ha...@st... wrote: >Thanks very much for spotting that, David. This was an easy fix. > >10.x.46c > >See Jmol-11-beta.zip 21-Aug-2006 19:46 and associated files in > > http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11 > >For the record, it was a failure of Jmol to do a (newly required) >"refresh" before the move or moveto command. > > > -- <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> David Marcey Fletcher Jones Professor of Developmental Biology Chair, CLU Biology Department 60 W. Olsen Rd., MC3700 Thousand Oaks, CA 91360 (805)-493-3263, 3590 ma...@cl... <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> |
From: <ha...@st...> - 2006-08-22 00:50:22
|
Thanks very much for spotting that, David. This was an easy fix. 10.x.46c See Jmol-11-beta.zip 21-Aug-2006 19:46 and associated files in http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11 For the record, it was a failure of Jmol to do a (newly required) "refresh" before the move or moveto command. |
From: David M. <ma...@cl...> - 2006-08-21 23:03:02
|
Apologies if you receive two copies of this...my email client is acting up. First, hearty thanks and kudos to Bob, et al. for all the great improvements and additions to Jmol since the 10.2 full release. I've been happily exploring the use of jvxl files in web-based macromolecular tutorial construction using some of the new pre-release versions. However, I've noticed some curious behavior with respect to spacefill commands when I run scripts that previously work fine in 10.2 (and older versions). Specifically, it seems that in some cases preceding move commands, spacefill is ignored until after the move when using newer pre-release versions of Jmol. If you are interested in helping with this, please compare the following two illustrations, the first uses 10.2, the second 10x38b. To see the effect, click on the 5th radio button, the one before "The connection between nucleotides in a DNA strand is thus referred to as a phosphodiester linkage.": http://www.callutheran.edu/Academic_Programs/Departments/BioDev/marcey/jmol_test/dna_intro_10_2/intro/start.html http://www.callutheran.edu/Academic_Programs/Departments/BioDev/marcey/jmol_test/dna_intro_10x_38b/intro/start.html Note that the spacefill on the phosphate groups disappears until the move is completed using v10x_38b. These tutorials are identical, except that the first calls 10.2 and the second uses 10x.38b. I get this with ALL post 10.2 versions, however. I'd be very interested to know if others are seeing seeing this in the above examples and if anyone else has run into this in their own work (I get it with both Firefox and IE6 in Windows). I also see the difference using Jmol.jar independently of a browser. The effect occurs with any pdb file. The effect dissapears if the move commands (move 5 15 2 -100 0 0 0 0 4; move 0 0 0 0 0 25 0 0 1) are removed. In this case, the effect is trivial, but for other illustrations, it would be really nice to get rid of this potential bug, if it is real. The full script is: "load atcg.pdb; background white; set frank off; select all; wireframe off; spacefill off; trace off; ribbons off; cartoons off; label off; monitor off; zoom 85; rotate x 180; rotate y -70; rotate x 30; move -5 -10 -2 100 0 0 0 0 .1; move 0 20 0 0 0 -25 0 0 .1; move 0 -25 0 0 0 0 0 0 .1; select all; wireframe 25; spacefill 75; select a; color [x5050ff]; select t; color [xe6e600]; select c; color [xe00000]; select g; color [x00c000]; select c; color cpk; define cbase atomno=50, atomno=51, atomno=52, atomno=53, atomno=54, atomno=55, atomno=56, atomno=57; select cbase; color [xe00000]; define csugar atomno=46, atomno=47, atomno=48, atomno=49, atomno=58, atomno=59, atomno=60; select csugar; color [x33CCFF]; define cphosphate atomno=42, atomno=43, atomno=44, atomno=45; select cphosphate; color cpk; select atomno=46; color [x999999]; delay 1; select all; color cpk; set specular on; set ambient 50; delay 1; select atomno=61, atomno=42, atomno=22, atomno=64, atomno=62, atomno=63, atomno=60, atomno=45, atomno=43, atomno=44, atomno=41, atomno=25, atomno=23, atomno=24, atomno=11, atomno=1, atomno=2, atomno=3, atomno=4; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25; delay .5; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25; delay .5; spacefill off; wireframe off; delay .5; wireframe 25; spacefill 75; move 5 15 2 -100 0 0 0 0 4; move 0 0 0 0 0 25 0 0 1; delay .5; select atomno=61, atomno=42, atomno=22, atomno=64, atomno=62, atomno=63, atomno=60, atomno=45, atomno=43, atomno=44, atomno=41, atomno=25, atomno=23, atomno=24, atomno=11, atomno=1, atomno=2, atomno=3, atomno=4; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25; delay .5; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25; delay .5; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25" Attached is the pdb used in the above examples if you want to try it with your applet. Cheers, and advance thanks, David -- <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> David Marcey Fletcher Jones Professor of Developmental Biology Chair, CLU Biology Department 60 W. Olsen Rd., MC3700 Thousand Oaks, CA 91360 (805)-493-3263, 3590 ma...@cl... <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> |
From: Frieda R. <fr...@ns...> - 2006-08-21 14:06:43
|
On Aug 21, 2006, at 7:21 AM, Rolf Huehne wrote: > Frieda Reichsman wrote: >> does anyone know if there a way >> to re-set Java's memory to avoid the "Java.lang out of memory error" >> that results from re-loading a page with an applet many times? >> <snip> > > The only definite way I know of, to free the memory of previous Jmol > page loads, is to quit the browser and usually automatically the > JavaVM > with it. Hi Rolf, Yes, this is what I seek to avoid. > Since it is not very nice, if you have to do this every 15 minutes, I > increase the maximum amount of memory the JavaVM is allowed to use. > Currently I am using 256 MB as default (having 1 GB physical memory), > but I already set it to 1.6 GB to be able to work (successfully) with > the largest PDB file available from RCSB (biological unit 1 of '2bvi', > 386 MB uncompressed file size) within my Jmol applet interface. > > In order to set the maximum memory size you must open the > configuration > dialog of your Java installation (I don't know where it is hidden on a > Mac). On Mac OSX there is a Java preferences pane accessed through Applications/Utilities/Java/J2SE 5.0/Java Preferences > Then there must be something like an 'Advanced Options' section > where you can type in some text. Although it is not under advanced, there is a form for entering text on the General section of the Java preferences. > If you want to set the memory size to > 256MB you have to type: > > -Xmx256m I just now entered this into the form on the General section, and will report back to the list when I have a sense of whether it is increasing the time between errors. > > You can exchange the '256' by any number you like, as long as it > doesn't > exceed the available virtual memory space. But it is better for the > overall performance of your computer to choose a value for your > everyday > work that is sufficient below the amount of physical memory (RAM). > > I can usually work quite a lot before I run into the 'out of memory' > problem with 256MB. But this depends of course of the size of the > structures you are loading and the number of reloads you perform. OK, excelllent info, I will update the list with my results in the next few days. Best, Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Rolf H. <rh...@fl...> - 2006-08-21 11:21:55
|
Frieda Reichsman wrote: > Which brings to mind this question - does anyone know if there a way > to re-set Java's memory to avoid the "Java.lang out of memory error" > that results from re-loading a page with an applet many times? > In my Java console (Linux or WinXP) there appears at the top a list of key commands. One is 'g' for garbage collection. But this will only help for a few addittional reloads. My strategy is to avoid reloading pages with Jmol applets but opening them up in new windows. I do this because I expect the browser to "kill" the applet if the corresponding window gets closed (at least Firefox definitely does not do this if you reload the applet). But from a comment Bob gave on this topic on the list a while ago I fear even that isn't true. The only definite way I know of, to free the memory of previous Jmol page loads, is to quit the browser and usually automatically the JavaVM with it. Since it is not very nice, if you have to do this every 15 minutes, I increase the maximum amount of memory the JavaVM is allowed to use. Currently I am using 256 MB as default (having 1 GB physical memory), but I already set it to 1.6 GB to be able to work (successfully) with the largest PDB file available from RCSB (biological unit 1 of '2bvi', 386 MB uncompressed file size) within my Jmol applet interface. In order to set the maximum memory size you must open the configuration dialog of your Java installation (I don't know where it is hidden on a Mac). Then there must be something like an 'Advanced Options' section where you can type in some text. If you want to set the memory size to 256MB you have to type: -Xmx256m You can exchange the '256' by any number you like, as long as it doesn't exceed the available virtual memory space. But it is better for the overall performance of your computer to choose a value for your everyday work that is sufficient below the amount of physical memory (RAM). I can usually work quite a lot before I run into the 'out of memory' problem with 256MB. But this depends of course of the size of the structures you are loading and the number of reloads you perform. Regards, Rolf |
From: Egon W. <ewi...@un...> - 2006-08-20 21:15:07
|
Hi, Ok, here are some first observations... On Sunday 20 August 2006 22:58, Mir Mohammed Assadullah wrote: > Here are the fragments: > > CRYSTAL1.XML: > > <molecule id="m1"> > <crystal z="4"> > <stm:scalar title="a" errorValue="0.001" > units="angstrom">4.500</stm:scalar> > <stm:scalar title="b" errorValue="0.001" > units="angstrom">4.500</stm:scalar> > <stm:scalar title="c" errorValue="0.001" > units="angstrom">4.500</stm:scalar> > <stm:scalar title="alpha" > units="degrees">90</stm:scalar> > <stm:scalar title="beta" > units="degrees">90</stm:scalar> > <stm:scalar title="gamma" > units="degrees">90</stm:scalar> > <symmetry id="s1" spaceGroup="Fm3m"/> > </crystal> > <atomArray> > <atom id="a1" elementType="Na" formalCharge="1" > xyzFract="0.0 0.0 0.0" xy2="+23.2 -21.0"/> > <atom id="a2" elementType="Cl" formalCharge="-1" > xyzFract="0.5 0.0 0.0"/> > </atomArray> > </molecule> Jmol might not be happy about the namespace prefix yet, but will need to verify that tomorrow. A question: does it show no atoms at all? If it would one Na and one Cl then that would be expected, because Jmol does not 'do' the symmetry yet. > ----------------------- > crystal1.html: > > <cml title="crystal example"> > <molecule id="m1"> > <crystal z="4"> > <scalar title="a" errorValue="0.001" > units="units:angstrom">4.500</scalar> > <scalar title="b" errorValue="0.001" > units="units:angstrom">4.500</scalar> > <scalar title="c" errorValue="0.001" > units="units:angstrom">4.500</scalar> > <scalar title="alpha" > units="units:degree">90</scalar> > <scalar title="beta" > units="units:degree">90</scalar> > <scalar title="gamma" > units="units:degree">90</scalar> > <symmetry id="s1" spaceGroup="Fm3m"/> > </crystal> > <atomArray> > <atom id="a1" elementType="Na" formalCharge="1" > xyzFract="0.0 0.0 0.0" xy2="+23.2 -21.0"/> > <atom id="a2" elementType="Cl" formalCharge="-1" > xyzFract="0.5 0.0 0.0"/> > </atomArray> > </molecule> > </cml> > > > ___________________________ > > crystal2.html: > > <molecule> > <crystal> > <scalar dictRef="cml:cryst.a">9.4620</scalar> > <scalar dictRef="cml:cryst.b">8.3920</scalar> > <scalar dictRef="cml:cryst.c">5.2210</scalar> > <scalar dictRef="cml:cryst.alpha">90.0000</scalar> > <scalar dictRef="cml:cryst.beta">110.1800</scalar> > <scalar dictRef="cml:cryst.gamma">90.0000</scalar> > <symmetry spaceGroup="C 2/C" convention="gulp"/> > </crystal> > <atomArray> > <atom id="a1" elementType="Li" xFract="0.0000" > yFract="0.2747" zFract="0.2500"/> > <atom id="a2" elementType="Al" xFract="0.0000" > yFract="0.9067" zFract="0.2500"/> > <atom id="a3" elementType="Si" xFract="0.2941" > yFract="0.0935" zFract="0.2560"/> > <atom id="a4" elementType="O" xFract="0.1097" > yFract="0.0823" zFract="0.1406"/> > <atom id="a5" elementType="O" xFract="0.3647" > yFract="0.2671" zFract="0.3005"/> > <atom id="a6" elementType="O" xFract="0.3566" > yFract="0.9867" zFract="0.0583"/> > </atomArray> > </molecule> In this fragment the namespaced unit cell dictRef's might be a problem, but would like to check that... Do unit cell axes for all examples? More on this later this week... Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: Mir M. A. <ass...@ya...> - 2006-08-20 20:59:52
|
Greetings: I tried to load the sample crystals listed at http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/ including CRYSTAL1.XML, crystal1.html, and crystal2.html. jmol loaded the latter two fine, but did not display the crystals. I am wondering if I need to add addtional markup than what is in the sample files or if I need to configure jmol properly. Regards, Assadullah __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
From: <ha...@st...> - 2006-08-20 20:58:12
|
Same cheat. (Really just loading an HTML file.) It's not that pop-ups don't work, it's that pop-ups that dump HTML code to the window instead of sending a page do not work. If no one comes up with a solution for the Mac bug (I have to say) that prevents on the fly writing HTML directly to a new window and having a LiveConnect applet, I will consider it a loss and cheat as well. :) Bob > One further example of (working) UI in Jmol applets in a pop-up > window in Safari: > > On Angel Herraez's page, > http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/v6_1/pop-up_Jmol.htm > > - select the radio button for generating a pop-up > - then click the link to view the structure > > the UI controls work in that pop-up window on Safari. > > Frieda > /////////////////////////////////////////// > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > > /////////////////////////////////////////// > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: <ha...@st...> - 2006-08-20 20:38:34
|
> > On Aug 18, 2006, at 9:24 PM, Bob Hanson wrote: > >> Frieda, what sort of surfaces are you particularly interested in >> displaying? >> >> Bob > > Solvent-accessible surfaces of macromolecules are what I am > accustomed to using vis Chime, hence what I am seeking to create. > However I have to admit that I am not aware of what the distinction > is between "isosurface" and solvent-accessible surface... There are two subtle distinctions now being made in Jmol -- "Solvent-accessible" which means the probe center position when rolled around the molecule. This is: isosurface SAsurface 1.2 where 1.2 is the solvent probe radius. "solvent-excluded" or "molecular" which means the set of all points on the solvent sphere that touch the Van der Waals radius along with the portions of the solvent sphere that form "caveties" when the solvent sphere touches the molecule at more than one point. This is: isosurface solvent 1.2 Both are called isosurfaces because they represent the points in space that have the same measurement, in this case the same distance from the solvent probe (and as described above). "SAsurface" display is far faster than "solvent" and probably what you want. Sorry, earlier I forgot about the SAsurface option. Bob > > Frieda > > > >> >> Frieda Reichsman wrote: >> >>> Hi All, >>> >>> I am interested in fast rendering of surfaces for large molecules. It >>> seems that Bob Hanson has invented a file format for this purpose, >>> called JVXL. I have seem Angel Herraez's and Bob's test pages for >>> surfaces, but I am still puzzled as to how to get started in doing >>> this. >>> >>> To create a JVXL surface file in Jmol, do you first have to load a >>> CUBE file into Jmol? I have started to read a little about CUBE files >>> but am unfamiliar with them. How do you generate a CUBE file? >>> >>> Frieda >>> >>> /////////////////////////////////////////// >>> >>> >>> Frieda Reichsman, PhD >>> >>> Molecules in Motion >>> >>> Interactive Molecular Structures >>> >>> http://www.moleculesinmotion.com >>> >>> >>> /////////////////////////////////////////// >>> >>> >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> --------------------------------------------------------------------- >>> ---- >>> Using Tomcat but need to do more? Need to support web services, >>> security? >>> Get stuff done quickly with pre-integrated technology to make your >>> job easier >>> Download IBM WebSphere Application Server v.1.0.1 based on Apache >>> Geronimo >>> http://sel.as-us.falkag.net/sel? >>> cmd=lnk&kid=120709&bid=263057&dat=121642 >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> ---------------------------------------------------------------------- >> --- >> Using Tomcat but need to do more? Need to support web services, >> security? >> Get stuff done quickly with pre-integrated technology to make your >> job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache >> Geronimo >> http://sel.as-us.falkag.net/sel? >> cmd=lnk&kid=120709&bid=263057&dat=121642 >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > /////////////////////////////////////////// > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > > /////////////////////////////////////////// > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: Frieda R. <fr...@ns...> - 2006-08-20 13:52:00
|
On Aug 20, 2006, at 5:26 AM, Hens Borkent wrote: > Isosurface became the name of the command in Jmol to generate > surfaces, > probably because the first surfaces were molecular orbitals. > Orbitals do > not have a particular size; the values of the function get smaller and > smaller with distance from the molecule, and surfaces are created by > connecting points with the same value. Hence isosurface. Same for > electron density, for which an isosurface can be drawn that coincides > more or less with the van der Waals surface. Or much smaller, or > larger, > depends on what feature you would like to show. > To solvent accessible surfaces this doesn't apply. There is only one, > given the radius of the solvent. > However, all these surfaces, spheres and so on are currently created > with the command isosurface. OK, very clear now! thanks much. Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Frieda R. <fr...@ns...> - 2006-08-20 13:50:54
|
One further example of (working) UI in Jmol applets in a pop-up window in Safari: On Angel Herraez's page, http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/v6_1/pop-up_Jmol.htm - select the radio button for generating a pop-up - then click the link to view the structure the UI controls work in that pop-up window on Safari. Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Frieda R. <fr...@ns...> - 2006-08-20 13:40:49
|
Hi Oja, Thanks for your reply. Any idea when Eclipse 3.2.1 might appear? I do not see anything on the Eclipse wiki that is helpful in that regard. I would not be developing Bioclipse - I enquired because I was interested in trying out Bioclipse to see if it would be useful in exploring macromolecules as I develop web-based Jmol tutorials. Any thoughts on that? Frieda On Aug 17, 2006, at 8:45 AM, Ola Spjuth wrote: > Hi Frieda, > > Bioclipse is developed in Java but relies on native SWT-libraries > and hence we need to distribute one version for each OS. > > We have had problems exporting correct packages for Mac OS X due to > a bug in Eclipse 3.2 and Apple's compatibility libraries, but this > should be fixed in the next Eclipse release (3.2.1). It is still > possible to develop Bioclipse on a Mac (I am!) with some > limitations in functionality. > > We hope to be able to offer a binary Mac OS X release very soon! > > See the wiki page http://wiki.bioclipse.net/index.php? > title=Bioclipse_on_Mac_OS_X for more information. > > Cheers, > > .../Ola > > On Aug 16, 2006, at 16:18 , Frieda Reichsman wrote: > >> Hi Ola, >> The Bioclipse download pages seem to say that Bioclipse is OS- >> independent. Can you tell me which version will run on Mac OSX? It >> seems one is marked for Linux and the other for Win... >> Frieda >> /////////////////////////////////////////// >> >> Frieda Reichsman, PhD >> Molecules in Motion >> Interactive Molecular Structures >> http://www.moleculesinmotion.com >> >> /////////////////////////////////////////// >> >> >> >> On Aug 11, 2006, at 10:26 AM, Ola Spjuth wrote: >> >>> The Bioclipse team is proud to announce the release of Bioclipse >>> 1.0, containing a Jmol plugin and a script editor for Jmol >>> scripts with syntax highlighting and code assistance. >>> >>> Bioclipse [1] is a free, open source, workbench for chemo- and >>> bioinformatics with powerful editing and visualization >>> capabilities for molecules, sequences, proteins, spectra etc. The >>> major features of version 1.0 are: >>> >>> * Import and export in various file formats >>> * Visual editing of molecular 2D-structures >>> * 3D-visualization of molecules and proteins >>> * Editing and visualization of sequences and features (DNA, RNA, >>> proteins etc) >>> * Graphing and editing of various types of spectra, e. g. NMR, MS >>> * Retrieval of resources (sequences, proteins, etc) from public >>> data repositories >>> * Scripting of 3D-visualizations with syntax highlighting and >>> content assistance >>> * PDB-editor with syntax highlighting for working with PDB files >>> * CMLRSS-viewer for downloading chemical content published on the >>> web using RSS-feeds >>> * Integrated, searchable help-system >>> * Hierarchical view of molecular and macromolecular substructures >>> and calculation of chemical properties >>> * Connection with external programs, e. g. PyMol >>> >>> Bioclipse is a rich client, which means it is run on your local >>> computer but also gives the possibility to communicate with >>> servers for data retrieval and computational services. The >>> powerful plugin architecture is based on Eclipse[2], and results >>> in a responsive, integrated user interface designed for simple >>> and intuitive operations that at the same time is easy to extend >>> with custom functionality. >>> >>> There is much ongoing work with Bioclipse and new features are >>> constantly added. Please visit the Bioclipse Wiki [3] in order to >>> get the latest information regarding the development. >>> >>> Bioclipse is available for download from Sourceforge [4]. >>> >>> [1] Bioclipse homepage: http://www.bioclipse.net >>> [2] Eclipse: http://www.eclipse.org >>> [3] Bioclipse Wiki: http://wiki.bioclipse.net >>> [4] Sourceforge project site: http://sourceforge.net/projects/ >>> bioclipse/ >>> >>> -------------------------------------------------------------------- >>> ----- >>> Using Tomcat but need to do more? Need to support web services, >>> security? >>> Get stuff done quickly with pre-integrated technology to make >>> your job easier >>> Download IBM WebSphere Application Server v.1.0.1 based on Apache >>> Geronimo >>> http://sel.as-us.falkag.net/sel? >>> cmd=lnk&kid=120709&bid=263057&dat=121642____________________________ >>> ___________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > ---------------------------------------------------------------------- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642______________________________ > _________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Frieda R. <fr...@ns...> - 2006-08-20 13:31:15
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On Aug 20, 2006, at 5:13 AM, David Leader wrote: > I've never looked at the Jmol console - thought it was for script > entry, but perhaps it gives error feedback too), Hi David, The Jmol console gives excellent and abundant feedback following the command, set debugscript on In this mode, Jmol responds to every command in one way or another. Great for debugging long script files. > > *The 'java console' was a convenience for pre-OSX Mac users, So this 'java console' must have been a Mac OS thing... The Java console I am using is provided by Java itself, and is accessed by using a Java preferences panel, where you can tell Java to open up its own console by default when it encounters an applet. The Java preferences interface can be opened by going to Applications/Utilities/Java/J2SE 5.0/Java Preferences Which brings to mind this question - does anyone know if there a way to re-set Java's memory to avoid the "Java.lang out of memory error" that results from re-loading a page with an applet many times? > because on other platforms error messages are generally directed to > 'system.out' which is the generic command line - in Windows it > would be the DOS command line, in unix it would be the unix command > line. It was built in to Netscape and IE5 (I think) as a place for > system.out errors and exceptions to go to, and if you had trouble > with an applet you could have a look at it to see what had > happened. In OSX there was no longer a need for this and it was > dropped, much to the initial puzzlement of many of us who were used > to it. > > As far as Javascript is concerned, there is no mechanism for > sending messages to system.out (perhaps for security reasons?) and, > as the javascript interpreter is built into the browser, one is > reliant on the browser-maker or third parties building debugging > consoles. That's why you'll see different error messages for the > same javascript error on different browsers. Yes, and it seems to me that Firefox provides a terrific js console, which usually gives much more specific and helpful error messages than Safari's. But I much prefer Safari's implementation of Jmol, so I only go to FF when I have an inscrutable js error in Safari's js console. Thanks for all the explaining, always good to supplement my knowledge of how Mac OS works. Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |