[Molvis-list] Advice on software

Wed Oct 11 08:23:15 EDT 2006

Dear Loren, 

We have developed a plug-in interface for PyMOL that we call EZ-Viz. We
designed it to work with macromolecules, but you may find it useful. You
can download it from

http://ez-viz.rit.edu

We have also created a help file to go with it.  

Paul Craig 

> -----Original Message-----
> From: 
> molvis-list-bounces+paul.craig=rit.edu at bioinformatics.org 
> [mailto:molvis-list-bounces+paul.craig=rit.edu at bioinformatics.
> org] On Behalf Of Loren Williams
> Sent: Tuesday, October 10, 2006 10:08 PM
> To: Molecular Visualization, especially in education with freeware
> Subject: Re: [Molvis-list] Advice on software
> 
> 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:
> 
> http://www.chem.wwu.edu/dept/facstaff/williams/courses/
> py_script_coords/index.html
> 
> Loren
> 
> 
> 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
> >>
> >> _______________________________________________
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> >> 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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