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