Re: [Jmol-users] Electron Density Maps & Clouds

[Eric Martz]

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:joel.suss...@weizmann.ac.il
>Web:www.weizmann.ac.il/~joel 
>www.weizmann.ac.il/ISPC 
>www.proteopedia.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/
>>
>>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
>>- - - - - - - - - - - - - - - - - - - - - - - - - - - */


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[Jmol-users] Electron Density Maps & Clouds

[Eric Martz]

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/

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® 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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