VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 30 2008 - 10:26:18 CST

Per,
  From your earlier note, you listed your Python version as being
2.4.3, but unless you've compiled VMD from source code, that is not
what you're using inside of VMD. The VMD 1.8.6 binaries we ship include
a Python 2.2 interpreter, which is what is being used when you run VMD,
irrespective of whatever environment variables you may have set. If you
have told VMD to use your Python 2.4.3 libraries, this may explain your
troubles. If you wish to use Python 2.4.3 rather than the Python 2.2
included in VMD 1.8.6, you'll need to compile VMD from source, which I
can help you with. If not, then you'll want to download the VMD Python
library tar file from the web site, and set the environment variables
as described in the User's Guide. Let me know if you need more help
with this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 30, 2008 at 05:13:38PM +0100, Per Jr. Greisen wrote:
> Hi,
>
> I remove the import but it gives me the same error for p.sasa(1.4) as stated
> earlier.
>
> Are there any ideas where to look for the conflict in the VMD installation -
> I have tested the other methods from the AtomSel class but they are working
> fine.
>
> Any advise appreciated
>
> On Jan 30, 2008 4:01 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
> > On Wed, 30 Jan 2008, Per Jr. Greisen wrote:
> >
> > PG> Hi Alex,
> >
> > per,
> >
> > thanks for the info.
> >
> > PG> My version of VMD is
> > PG>
> > PG> VMD for LINUX, version 1.8.5-rpm-FC5 (August 25, 2006)
> > PG>
> > PG> I use the class AtomSel using the following
> >
> > PG> from Scientific.Geometry import *
> >
> > please try removing this import (^^^^^)
> > you are not using any of those features.
> > perhaps there is a conflict in some of the code in there
> > with your VMD installation.
> >
> > the rest of the script works for me (using the latest alpha
> > version). please note, that AtomSel is deprecated as of VMD
> > 1.8.6 and is likely to go away at some time in the future.
> >
> > cheers,
> > axel.
> >
> > PG> import Molecule as mol
> > PG> import AtomSel as sel
> > PG> m = mol.Molecule()
> > PG> m.load('min_solvent.pdb')
> > PG> p = sel.AtomSel('protein')
> > PG> p.align()
> > PG> p.sasa(1.4)
> > PG>
> > PG> which gives me the runtime error. I check the code in line 158 but it
> > looks
> > PG> fine to me. My version of python is
> > PG> Python 2.4.3 (#1, Mar 14 2007, 18:51:08)
> > PG> [GCC 4.1.1 20070105 (Red Hat 4.1.1-52)] on linux2
> > PG>
> > PG> Any advise or help appreciated
> > PG> Thanks in advance
> > PG>
> > PG> Best
> > PG> Per
> > PG>
> > PG>
> > PG>
> > PG>
> > PG>
> > PG> On Jan 29, 2008 6:19 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> > wrote:
> > PG>
> > PG> > On Tue, 29 Jan 2008, Per Jr. Greisen wrote:
> > PG> >
> > PG> > PG> Hi,
> > PG> >
> > PG> > hi per,
> > PG> >
> > PG> > PG> I am using the SASA script in python to calculate some
> > solvations
> > PG> > properties
> > PG> > PG> - when I execute the command I get the following error tmp.sasa
> > PG> >
> > PG> > please be more specific. which script, which version of VMD,
> > PG> > which platform (which python, if applicable)?
> > PG> > without this information, it will be hard to track down your
> > PG> > problems. please keep in mind, that anybody willing to check
> > PG> > out what is happening must first be able to reproduce your problem.
> > PG> >
> > PG> > PG>
> > PG> > PG> File "VMD", line 1, in ?
> > PG> > PG> File "/usr/lib/vmd/scripts/python/AtomSel.py", line 158, in
> > sasa
> > PG> > PG> self.__list, **kwds)
> > PG> > PG> RuntimeError: more keyword list entries than argument specifiers
> > PG> >
> > PG> > i am not a python expert, but this looks a lot like the script
> > PG> > is incompatible with your version of VMD or python. did you check
> > PG> > the code in line 158?
> > PG> >
> > PG> > cheers,
> > PG> > axel.
> > PG> >
> > PG> > PG>
> > PG> > PG> How to resolve this error - any advise or help appreciated.
> > PG> > PG>
> > PG> > PG> Thanks in advance
> > PG> > PG>
> > PG> > PG> Best
> > PG> > PG>
> > PG> > PG> Per
> > PG> > PG>
> > PG> >
> > PG> > --
> > PG> >
> > =======================================================================
> > PG> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> > http://www.cmm.upenn.edu
> > PG> > Center for Molecular Modeling -- University of Pennsylvania
> > PG> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> > 19104-6323
> > PG> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> > 1-215-898-5425
> > PG> >
> > =======================================================================
> > PG> > If you make something idiot-proof, the universe creates a better
> > idiot.
> > PG> >
> > PG>
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078