Re: [Jmol-users] Electron Density Maps Clouds
Try a reload, clear cache, etc. It works fine for me in Safari or Firefox on OS X, default java memory (100 Mb). I can display both pages (cloud and maps) concurrently. Let me know if you continue to have problems! Is your connection to umass.edu slow? -E At 4/18/10, Prof. Joel L. Sussman wrote: 18-Apr-2010 9:00am Rehovot Dear Eric Idea sounds really good but JAVA never finishes loading on these two pages are they that big? joel -- Prof. Joel L. Sussman Pickman Professor of Structural Biology Director, The Israel Structural Proteomics Center Dept. of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL Tel: +972 8-934 4531 Fax: +972 8-934 6312 E-mail:mailto:joel.suss...@weizmann.ac.iljoel.suss...@weizmann.ac.il Web:http://www.weizmann.ac.il/~joelwww.weizmann.ac.il/~joel http://www.weizmann.ac.il/ISPCwww.weizmann.ac.il/ISPC www.http://proteopedia.orgproteopedia.org -- On 18 Apr 2010, at 07:42, Eric Martz wrote: I have not finished my testing to verify that Jmol 12.0 is displaying CCP4 electron density maps correctly, default isomesh at 1.0 sigma, but my preliminary tests are consistent with it functioning correctly. Meanwhile, for teaching tomorrow, I have whipped together an adaption of Bob Hanson's wonderful cloud representation of electron density maps. This will help to convey to beginners what the isomesh represents. http://www.umass.edu/molvis/edm/cloud/http://www.umass.edu/molvis/edm/cloud/ At the bottom of that page is a link to a 2.0 Angstrom EDM page. Don't miss the comparison of low and high temperature factor sections of the map. Also there is a quick and dirty start at what could become a Jmol based tool for exploring any map vs. model. http://www.umass.edu/molvis/edm/cloud/edm2.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Workshops: http://workshops.molviz.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://list.molviz.org Protein Explorer - 3D Visualization: http://proteinexplorer.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ -- Download Intel#174; 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Webcite and Jmol
Can anyone cast light on the issue described at http://www.ch.ic.ac.uk/rzepa/blog/?p=1930 ? -- +44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). -- Download Intel#174; 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] model to variable question
Does anyone know if a the molfile of a loaded model can be put into a Jmol variable inside of a Jmol script. By this, I mean that I would like to leave JavaScript out of the molfile extraction. To be a bit more specific, I am loading a model from a files inside of a Jmol script. After loading that model, can I put its molfile into a Jmol variable? Otis -- Otis Rothenberger chemagic.com -- Download Intel#174; 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] model to variable question
If it is just a mol file, you can use within Jmol:
var jmolx = getProperty(extractModel)
or from JavaScript:
var jsx = jmolEvaluate(getProperty('extractModel'))
Is that what you are after?
On Sun, Apr 18, 2010 at 7:29 PM, Otis Rothenberger osrot...@chemagic.comwrote:
Does anyone know if a the molfile of a loaded model can be put into a
Jmol variable inside of a Jmol script. By this, I mean that I would like
to leave JavaScript out of the molfile extraction. To be a bit more
specific, I am loading a model from a files inside of a Jmol script.
After loading that model, can I put its molfile into a Jmol variable?
Otis
--
Otis Rothenberger
chemagic.com
--
Download Intel#174; 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
___
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--
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#174; 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___
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Re: [Jmol-users] model to variable question
Bob, Thanks. This is the one I wanted: On 4/18/2010 10:09 PM, Robert Hanson wrote: If it is just a mol file, you can use within Jmol: var jmolx = getProperty(extractModel) Otis -- Otis Rothenberger chemagic.com -- Download Intel#174; 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
