VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jan 30 2008 - 10:28:57 CST

john,

if you look at the whole conversation, you'll see that per is using
the vmd 1.8.5 rpm compiled on fedora 5 from the contrib section.
that python should match.

axel.

On Jan 30, 2008 11:26 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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
>
> 

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