[Molvis-list] Advice on software

Wed Oct 11 19:52:39 EDT 2006

On Oct 11, 2006, at 4:59 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.

In principle, it should work fine on a mac under X11, right? That's  
what I use
whenever I want to use pymol plugins.

> 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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>>>>> https://bioinformatics.org/mailman/listinfo/molvis-list
>>>>
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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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