Re: [Jmol-users] File size limit

default -Xms and -Xmx (initial and max values) Try something like java -Xms1024M -jar Jmol.jar Nico On Thu, Oct 18, 2012 at 10:43 AM, Inbal Tuvi-Arad inba...@openu.ac.il wrote: Hello to all, I'm using Jmol stand-alone version to follow molecular dynamics results. The files are very big

[Jmol-users] File size limit

Hello to all, I'm using Jmol stand-alone version to follow molecular dynamics results. The files are very big with over 100,000 molecules each, in xyz format. Jmol does not open them unless I cut them into small pieces of about 5000-1 molecules, depending on the number of atoms. Is there a

Re: [Jmol-users] Drawing symmetry elements across models

symmetry element was found. Thank you Bob and Dean for developing this cool feature! All the best, Inbal ___ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel 1 University Road., POB 808 Raanana 43107 ISRAEL Tel: 09

Re: [Jmol-users] Drawing symmetry elements across models

) {draw pointgroup;if (_modelNumber == _lastframe){break};frame next} On Mon, Jul 4, 2011 at 1:01 AM, Inbal Tuvi-Arad inba...@openu.ac.il wrote: Dear Bob, Thank you for your answer. If I understand correctly, once the bug is fixed - if I have 10 models in my file I would need to type 10 lines

Re: [Jmol-users] Drawing symmetry elements across models

pointgroup frame 1.2;select 1.2;draw pointgroup ... like that. Please let me know if that works or not. Bob Hanson On Sun, Jul 3, 2011 at 2:28 AM, Inbal Tuvi-Arad inba...@openu.ac.il wrote: Hello to all, I'm working with xyz files that contains several models of the same molecule. I'd like

[Jmol-users] Drawing symmetry elements across models

Hello to all, I'm working with xyz files that contains several models of the same molecule. I'd like to be able to present the symmetry elements of all models so that navigation between them will keep the symmetry elements. Draw pointgroup only works for the current model. Is there a command

Re: [Jmol-users] Chime to Jmol translation

Hello Angel, Thank you for your help. I will consider seriously your last offer! :) Best wishes, Inbal -Original Message- From: Angel Herraez [mailto:angel.herr...@uah.es] Sent: Monday, February 16, 2009 4:03 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Chime to

[Jmol-users] Chime to Jmol translation

Dear Jmol users, We have several old web pages written for the Chime plug-in that we would like to translate to Jmol. Are there any automatic tools that can do that, at least partially? Sincerely, Inbal -- Open Source

[Jmol-users] Continuous Symmetry Measures - A new website

of Israel. I would be very grateful for any feedback, suggestions or comments regarding the website. Sincerely, Inbal __ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel 108 Ravutski St., POB 808, Raanana, 43107, Israel

Re: [Jmol-users] Problem with display of pdb file

reader for 10.x.16. You could try that instead. Bob Hanson Inbal Tuvi-Arad wrote: Hello to all, I have a problem with the way Jmol displays pdb files and hope someone can help me. I downloaded a pdb file from the CSD. When I open it in Jmol I can not see all the chemical bonds and some

[Jmol-users] Problem with display of pdb file

see all the bonds. What could be the reason? Following is a copy of the file. Sincerely, Inbal Tuvi-Arad __ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel 108 Ravutski St., POB 808, Raanana, 43107, Israel Tel: 972-9-778-1773 Fax