VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 09 2010 - 10:54:06 CST

Thomas,
  The easiest way is to load your PDBs one at a time into a second molecule,
reading their respective beta columns via "$sel get beta", and then using
"$sel set user" to set the user data in the first molecule. It would be
a simple foreach loop over your PDB files loading copying their beta
fields into the first molecule's user fields.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 09, 2010 at 05:50:01PM +0100, Thomas Steinbrecher wrote:
> Hi John,
>
> thanks for the info, that explains it. I looked at Axels tutorials, he
> only describes reading data from an external file into the molecule or
> how to put calculated data into the user field. Im not very experienced
> at vmd scripting, how would I access the beta field of each frame in
> such a script?
>
> Kind Regards,
>
> Thomas
>
> Quoting John Stone <johns_at_ks.uiuc.edu>:
>
> >
> >Thomas,
> > The issue is that in VMD, the "beta" field is not stored independently
> >for each timestep, but rather once per molecule. You can load the beta
> >field into one of the "user" per-atom-per-timestep fields however to do
> >what you have in mind. I believe this is discussed in one of the VMD
> >tutorials (maybe Axel's CPMD/VMD tutorial if I remember right?)
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Mar 09, 2010 at 05:26:16PM +0100, Thomas Steinbrecher wrote:
> >>Dear vmd users,
> >>
> >>I am puzzled what I am doing wrong here:
> >>
> >>I have a trajectory (one file of multiple pdb snapshots of the same
> >>molecule separated by END cards) along which a property of my molecule
> >>changes. The value of that property for each atom is written in the
> >>beta column of the pdbs.
> >>
> >>When I load the file, it recognizes the number of frames and when I set
> >>the color representation to 'beta', the first frame is colored
> >>correctly. However, when I view the trajectory, the colors dont change,
> >>even if I set 'update color every frame' in the trajectory tab (yes,
> >>the actual numbers in the pdb do change).
> >>
> >>Is there something obvious I am missing? Im using vmd 1.8.6 btw.
> >>
> >>Kind regards,
> >>
> >>Thomas
> >>
> >>Dr Thomas Steinbrecher
> >>Universität Karlsruhe
> >>Inst. f. phys. Chemie Abt Theor. Chem. Biol.
> >>Vincenz-Prießnitz-Str. 1
> >>76131 Karlsruhe, Germany
> >>phone ++49 721 608 5703
> >>fax ++49 721 608 5710
> >>
> >
> >--
> >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
> >
>
>
>
> Dr Thomas Steinbrecher
> Universität Karlsruhe
> Inst. f. phys. Chemie Abt Theor. Chem. Biol.
> Vincenz-Prießnitz-Str. 1
> 76131 Karlsruhe, Germany
> phone ++49 721 608 5703
> fax ++49 721 608 5710
> 

-- 
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