[Molvis-list] Advice on software

Eric Martz emartz at microbio.umass.edu
Tue Oct 10 17:32:13 EDT 2006

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: 

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. 


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: 

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
>Emmanuel College
>kowitj at emmanuel.edu
>Molvis-list mailing list
>Molvis-list at bioinformatics.org

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz

Biochem 3D Education Resources http://MolviZ.org
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Protein Explorer - 3D Visualization: http://proteinexplorer.org
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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
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