The Mac functionality would be critical for hands on teaching, if you are going to have the kids do things on their own. It seems macs have really made a come back with undergraduates. I hope you can work around the plug-in issue. Loren On Oct 11, 2006, at 1:59 PM, Paul A Craig wrote: > 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 >>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - */ >>>>> >>>>> _______________________________________________ >>>>> 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 >> _______________________________________________ >> 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