From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jan 30 2008 - 09:01:21 CST

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.