Re: [Jmol-users] model to variable question

[Otis Rothenberger]

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




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Re: [Jmol-users] model to variable question

[Robert Hanson]

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 wrote:

> 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® 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.
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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
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[Jmol-users] model to variable question

[Otis Rothenberger]

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




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[Jmol-users] Webcite and Jmol

[Rzepa, Henry]

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). 



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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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