[Molvis-list] Script for saving files in Chime

Inbal Tuvi-Arad inbaltu at openu.ac.il
Mon Jan 10 07:37:17 EST 2005

Dear Eric,
 Thank you for your answers.  We tried to see if Jmol will be suitable for
our needs but it seems that it doesn't have other capabilities that we need:
one is the ability to load pmesh files and the other is to load a pdb or any
other molecular file from the user's computer.  We are therefore working
with Chime, trying to build the script in such a way that when these
features will be added to Jmol we will be able to convert easily. 

  As for your suggestion about PE - we are not dealing with proteins or
macromolecules in general, so marking part of  the molecule is not a
relevant feature for us.  Our project has to do with molecules of under 20
atoms.  But, I still enjoyed the demos you sent.

Best regards,


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: 972-9-778-0661
Email: inbaltu at openu.ac.il

> -----Original Message-----
> From: molvis-list-bounces at bioinformatics.org 
> [mailto:molvis-list-bounces at bioinformatics.org] On Behalf Of 
> Eric Martz
> Sent: Tuesday, January 04, 2005 11:42 PM
> To: Molecular Visualization, especially in education with freeware
> Subject: Re: [Molvis-list] Script for saving files in Chime
> At 12/28/04, you wrote:
> >Dear colleagues,
> >   We are working on a Chime based project that requires 
> loading a molecule
> >from the hard disk, manipulating its coordinates by an 
> external code and
> >saving the new structure.  We would like to know if there is a way to
> >control Chime's "Save Molecule As" function through the 
> Chime script.  We
> >want to have a button on our Website which, using JavaScript 
> and Chime's
> >script, will open the "Save Molecule As" dialog box and 
> enable the user to
> >save the current molecule to his/her hard disk. We know it 
> is possible in
> >Rasmol.  Is this possible in Chime?
> >
> >Best wishes,
> >Inbal
> Dear Inbal:
> The "save" commands from RasMol were disabled for security 
> reasons when the 
> RasMol code was ported to Chime. The only PDB file save from 
> Chime is via 
> Chime's menu (click on MDL, File, Save Molecule As). This 
> always saves the 
> PDB file exactly as it was received, including the original 
> header, and 
> without any changes regardless of what is selected or 
> rotations, etc. (see 
> http://www.umass.edu/microbio/rasmol/pdbtools.htm). (Actually 
> there is a 
> bug in Chime -- sometimes it saves the most recent command 
> script instead 
> of the PDB file.)
> So I don't think you can put a button in a web page that will 
> initiate the 
> save dialog with Chime, but you can simply explain how to use 
> Chime's menu 
> to do this (3 clicks instead of one).
> It may be possible to do what you want with the Jmol applet. 
> Can someone 
> confirm and give details? Jmol is open-source and understands 
> essentially 
> all Chime script commands (except not yet surfaces). It comes 
> from your 
> server instead of the client having to install a plugin. It 
> is already more 
> flexible and powerful than Chime in most areas. www.jmol.org
> -Eric
> ----
> Eric Martz, Professor Emeritus, Dept Microbiology
> University of Massachusetts, Amherst MA US
> http://www.umass.edu/molvis/martz
> _______________________________________________
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