VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jun 29 2009 - 08:51:01 CDT

On Mon, 2009-06-29 at 12:29 +0200, Bjoern Olausson wrote:

hi bjoern,

> Could you redirect me to some VMD 1.8.7 <-> Python tutorial? I would like to
> stick to python as much as possible ;-)

since the python support in VMD is so restricted this is probably
not the best way to understand "the VMD way". almost all documentation
that is available is in the user's guide. many of the more sophisticated
analysis scripts and methods are written in tcl. by sticking to python,
you will limit yourself and get only a restricted impression of the
capabilities of VMD. now the repeated requests for python enabled
binaries, show that there are people out there that use the python
interface in VMD a lot, but almost nobody has published any plugins
or script libraries that can be re-used by others. i learned most of
what i know about smart VMD scripting from studying other people's
tcl scripts.

[...]

> And while I am on it... I am writing a small python script which can combine
> multiple output files and selectively plot whatever is plotable ;-)
>
> For this reason I was looking around for the formating of the output file.
> Something like that link below for PDB-files:
> http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ATOM
>
> Especially I am interested in the formating and naming of the columns of this
> part:
>
> PRESSURE: 29109200 546.983 413.11 92.8291 413.11 -486.118 30.045 92.8291
> 30.045 -566.529
> GPRESSURE: 29109200 388.5 383.831 6.4171 339.175 -407.812 358.594 -111.003
> -223.426 -491.163
> PRESSAVG: 29109200 32.2755 -27.1969 -120.07 -27.1969 8.01839 -60.9932 -120.07
> -60.9932 -3.92224
> GPRESSAVG: 29109200 30.6858 -30.7705 -117.957 -14.7335 12.1397 -64.4612
> -123.885 -49.5245 -4.49357
> ENERGY: 29109200 2828.8126 8444.6120 4596.9095 59.0735
> -39328.9221 -1866.4500 0.0000 0.0000 13455.6967
> -11810.2678

sorry, this doesn't make any sense to me. you seem to be quoting part
of a NAMD output file, but that has _nothing_ to do with the protein
database atomic file format.

if you want to plot the data from a simulation run, have a look at
the namd plot plugin already bundled with VMD. no need to re-invent
that wheel again. ;)
http://www.ks.uiuc.edu/Research/vmd/plugins/namdplot/

cheers,
   axel.

> Thanks for your help
>
> greeting
> Bjoern 

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