Re: [PyMOL] PymOl INstallation PRoblems

Tue, 11 Apr 2006 10:35:10 -0700 

My dear PyFriends,

OKay, I was able to successfully get Pymol up and running on Sony Vaio, thanks 
to my new friend Chris Yip!  Thanks a million!  Hip-Hip Hurray!

The cure you ask?  Well, as Chris mentioned in his suggestions, I simply went 
to the Sony website and downloaded the update driver for the graphics 
controller.  The funny thing was that, it wasn't nVidia, it was ATI.  So 
apparently, this driver issue may not be primarily an nVidia issue.  But after 
I installed updated driver and restarted, Pymol ran beautifully.  Now, I assume 
we may still run across some bugs in the future, but for today, we feast on 
victory!

Thanks again Chris and I hope this helps someone else in the future!  



Cheers,
Nick




Couple of things that people tried - one was to go to an older PyMol version 
(and the corollary - go to the latest beta version).


we did try some drivers from the various vendors but that was also hit and 
miss...


There didn't seem to be a consistent fix


Chris




On Apr 10, 2006, at 4:47 PM, Noinaj wrote:


  Thanks Chris for your help.  As you have noted and as I have read online, 
there seems to be a problem with the graphics drivers, is this correct?  Do you 
know if updating the drivers remedied the problem?  If not, were you able to 
work around the problem?  Thanks again for your help!


  Cheers,
  Nick



    ----- Original Message -----
    From: Christopher Yip
    To: Noinaj
    Sent: Monday, April 10, 2006 4:31 PM
    Subject: Re: [PyMOL] PymOl INstallation PRoblems


    A lot of my students ran into the same problem this past fall - there are a 
bunch of notes on the list regarding nVidia graphics drivers that seem to be at 
the root cause of the problem - you might want to try a search under WinXP and 
Pymol...      


    http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4368.html 


    here are some of the links that I found were of use, and posted to my class 
list


    Check here for some info and suggestions:


    http://delsci.com/beta/


    Specifically..


    Take a look here:
    http://sourceforge.net/mailarchive/message.php?msg_id=11962703
    ++++++


    If anyone else is experiencing a non-functional PyMOL with late-model nVidia
    drivers on Windows XP or similar, pymol-0_99beta96 contains a workaround
    that has been reported to eliminate the problem.


    http://delsci.com/beta


    Hopefully the next driver release for Windows will fix this problem just
    like it did on Linux...
    +++++


    Some may find this useful too - a Wiki with hints:


    http://www.pymolwiki.org/index.php/Main_Page


    http://pymol.sourceforge.net/faq.html


    http://www.rubor.de/bioinf/pymol_tips.html






    On Apr 10, 2006, at 4:23 PM, Noinaj wrote:


      Hi PyWorld,


      I have been trying to help a friend install PyMol on her laptop (Sony 
Vaio) that has Windows XP Home Edition.  The installation runs smooth with no 
problem at all.  But once we try to open the program, its seems to stall, then 
crashes, and Windows XP asks if we would like to send a error report???

      I have searched the archives and online for answers, but with no luck.  
Therefore, I present to you, my PyFriends, our dilemma and seek a remedy to our 
problem.  I give you my word, my good friends, that upon finding the solution, 
I will not take all the credit for solving this mystery....just kidding, credit 
will be duly noted.

      Thanks in advance for any and all help!


      Cheers,
      Nick







    Christopher M. Yip, Ph.D., P.Eng.
    Associate Professor - Canada Research Chair in Molecular Imaging
    Department of Chemical Engineering and Applied Chemistry
    Department of Biochemistry
    Institute of Biomaterials and Biomedical Engineering
    The Terrence Donnelly Centre for Cellular and Biomolecular Research
    University of Toronto
    Room 404 160 College St.
    Toronto, ON, CANADA M5S 3E1
    (416) 978-7853
    (416) 978-4317 (fax)
    christopher....@utoronto.ca
    http://bigten.med.utoronto.ca








Christopher M. Yip, Ph.D., P.Eng.

Associate Professor - Canada Research Chair in Molecular Imaging

Department of Chemical Engineering and Applied Chemistry

Department of Biochemistry

Institute of Biomaterials and Biomedical Engineering

The Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

Room 404 160 College St.
Toronto, ON, CANADA M5S 3E1
(416) 978-7853

(416) 978-4317 (fax)

christopher....@utoronto.ca

http://bigten.med.utoronto.ca

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