VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jan 30 2008 - 10:24:55 CST

On Jan 30, 2008 11:13 AM, Per Jr. Greisen <pgreisen_at_gmail.com> 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 -

dunno. i finally found an old machine with the same vmd version and it
has the same error with the sasa method. interestingly, there is no significant
change in the python code, so it can only mean two things.
that there could be a python incompatibility (i tested a vmd compiled on
fedora 5 with a machine running fedora 6) or a bug in vmd that got
subsequently fixed. python support is always a bit shaky, since there is
much less people using it compared to tcl. perhaps one of the vmd/python
experts can comment on this issue.

you may have more luck with a newer version of VMD, but then you probably
cannot use those add-on molecules anymore. :-(

cheers,
    axel.

> 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.
> >
>
> 

-- 
=======================================================================
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.