[Molvis-list] Advice on software
Paul A Craig
pac8612 at rit.edu
Wed Oct 11 16:59:45 EDT 2006
Hi Judy,
We are employing a plug-in with PyMOL. To date the Mac does not support
plug-ins, so we are looking at a workaround. The latest versions appear
to function well in Linux, but that is not a help to Mac users.
Paul
> -----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 Judith Voet
> Sent: Wednesday, October 11, 2006 10:16 AM
> To: Molecular Visualization, especially in education with freeware
> Subject: Re: RE: [Molvis-list] Advice on software
>
> 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
> > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - */
> > > >
> > > > _______________________________________________
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> > >
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>
>
> --
> 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
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