[Molvis-list] Advice on software

Loren Williams loren.williams at chemistry.gatech.edu
Wed Oct 11 17:42:44 EDT 2006


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
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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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