From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Wed Jan 30 2008 - 10:13:38 CST

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.
>