[Molvis-list] Advice on software

Loren Williams loren.williams at chemistry.gatech.edu
Tue Oct 10 22:07:37 EDT 2006

re: payment for pymol

I just had my entire gen chem section of 96 students (none with AP  
chem) download and install pymol. The pymol web page is sort of  
confusing on this subject but in truth students and academics are  
allowed free download of ready to run versions of Pymol. Just ignore  
all the chatter about subscriptions and download it.

I have instructions, sample coordinate files and some scripts  
suitable for beginning gen chem students posted here:



On Oct 10, 2006, at 2:32 PM, Eric Martz wrote:

> Dear Joel,
> Most of us who have worked extensively with Chime (and RasMol) now  
> view Jmol (FREE) as the optimal replacement for Chime. Because it  
> is a java applet, it can produce molecular views in web browsers  
> just like Chime -- but the user does NOT need to install anything*,  
> and Jmol works in Safari or Firefox on Mac OSX (Intel or PPC),  
> Internet Explorer or Firefox on Windows, and Firefox on linux.  
> http://jmol.org
> *  (Java must be installed, but is already present on OSX and most  
> Windows computers, and is easily upgraded FREE at http://java.com)
> Jmol understands nearly the complete Chime command language, and  
> therefore is easy to script for those familiar with Chime or RasMol  
> scripting. For example, Protein Explorer (in Chime) records the  
> Chime scripts for the views in a session, and exports them into  
> MolSlides in **Jmol** with only minor modifications to the recorded  
> scripts.
> Chime sites can be converted to Jmol. I have not done this myself  
> so I'll leave it to others to advise the best guides/resources for  
> this.
> FirstGlance in Jmol (http://firstglance.jmol.org), also FREE, is a  
> very user-friendly basic protein structure exploration tool along  
> the lines of Protein Explorer, except not as powerful and not  
> having as much help for protein structure novices.
> In my opinion, FirstGlance in Jmol is better than the within- 
> browser and java-based viewers offered by the RCSB PDB (others  
> please add your opinions here). I can send you a point by point  
> comparison if you wish. But just spending half an hour or so with  
> each should be enough to convince you.
> As mentioned above, any view that can be obtained in Protein  
> Explorer (using Chime) can be saved into a MolSlide using **Jmol**.  
> This is a good way for professors to create rotatable zoomable  
> views that can be put on-line for their classes, or projected in  
> lectures. Learning to use Protein Explorer can take a day or more,  
> but once you do that, saving MolSlides is just a few mouse clicks.  
> Examples in Jmol: (http://molslides.proteinexplorer.org).
> Jmol can also do animations. I made my first recently showing the  
> conformational change when avian flu N1 binds Tamiflu (http:// 
> www.umass.edu/molvis/martz/lectures/labmolgen/). Other examples are  
> available from those more knowledgable than myself.
> ConSurf colors proteins by evolutionary conservation automatically.  
> Its results can now (as of a few weeks ago) be viewed in  
> FirstGlance in Jmol. (http://consurf.tau.ac.il)
> -------------
> PyMol has become extremely popular and is worth a careful look. It  
> is a stand-alone program with far more gorgeous rendering than  
> RasMol, Chime, or Jmol. It is very powerful but its documentation  
> is a bit out of date and it has a steeper learning curve, and less  
> automatically-displayed context-sensitive help than FirstGlance in  
> Jmol. PyMol works on all popular computer platforms.
> Although payment is required to download ready-to-run copies of PyMol,
> "Subscriptions are not required for full-time students or for usage  
> in teaching full-time students" as stated here: (http:// 
> www.pymol.org/funding.html).
> Regards, -Eric
> (Others on this list should feel free to offer views contrary to my  
> assertions above!)
> At 10/10/06, you wrote:
>> Hi.  For some time now I've used RasMol and Chime in introductory  
>> biology
>> lab for molecular visualizations and basic analysis of proteins.   
>> It seems
>> that RasMol is not compatible with new Macs, and there are some  
>> excellent
>> Chime tutorials that are not compatible with Firefox or IE.  My Mac
>> students are using iMol.  Other than downloading Netscape 4.x for  
>> the PCs,
>>  I'd appreciate suggestions on more recent software that is  
>> compatibile
>> with Chime tutorials and will allow protein analysis and movie  
>> making, and
>> maybe have more capabilities.  Thanks.
>> Joel Kowit
>> Biology
>> Emmanuel College
>> kowitj at emmanuel.edu
>> _______________________________________________
>> Molvis-list mailing list
>> Molvis-list at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/molvis-list
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://www.umass.edu/molvis/martz
> Biochem 3D Education Resources http://MolviZ.org
> See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> Workshops: http://workshops.proteinexplorer.org
> World Index of Molecular Visualization Resources: http:// 
> molvisindex.org
> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.proteinexplorer.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list):
>       http://bioinformatics.org/mailman/listinfo/molvis-list
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