[Molvis-list] Advice on software

Wed Oct 11 10:16:00 EDT 2006

Hi Paul,
Your paper describing EZ-Viz will appear in the Nov-Dec issue of
Biochemistry and Molecular Biology Education. It is a great step
toward making PyMOL more user-friendly. At the moment the plug-in is
only supported by
Windows and Linux versions of PyMOL. How are plans coming for making
it available for Mac users?
Cheers,
Judy

On 10/11/06, Paul A Craig <pac8612 at rit.edu> wrote:
> 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
> > >>
> > >> _______________________________________________
> > >> 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
> > > - - - - - - - - - - - - - - - - - - - - - - - - - - - */
> > >
> > > _______________________________________________
> > > Molvis-list mailing list
> > > Molvis-list at bioinformatics.org
> > > https://bioinformatics.org/mailman/listinfo/molvis-list
> >
> > _______________________________________________
> > Molvis-list mailing list
> > Molvis-list at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/molvis-list
> >
> _______________________________________________
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/molvis-list
>
>

-- 
Judith G. Voet, J. H. Hammons Professor, Emerita
Department of Chemistry
Swarthmore College
500 College Avenue
Swarthmore, PA 19081-1390
jvoet1 at swarthmore.edu
610-328-8520    	       	
FAX 610-328-7355