VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 07 2006 - 17:08:12 CST

Hi,
  If you've loaded the multi-structure PDB file as a trajectory,
then you can use the "mol drawframes" command to tell VMD how many of the
timesteps to superimpose at once, for a specific representation, e.g.:
  mol drawframes top 0 "0:29"

  John Stone
  vmd_at_ks.uiuc.edu
 

On Thu, Nov 02, 2006 at 03:23:41PM -0500, Adrian Kaats wrote:
> John,
>
> Thank you, that is exactly what I was looking for.
>
> Is there a set of commands (at the vmd command line, that is, without going gui), or something similar to mergemultiframe.tcl that can be used to display a subset of available frames?
>
> Just for calrification, MODELs in a PDB are treated as frames in VMD?
>
> Thank you very much,
>
> Adrian
>
> John Stone <johns_at_ks.uiuc.edu> wrote:
> Adrian,
> The "biological unit coordinate files" produced by the PDB are essentially
> several PDB files concatenated together. VMD treats these as a trajectory
> (for historic reasons, and as a means of interchange with other software)
> so to display the entire structure (without any scripting), you'll
> need to select the "trajectory" tab in the graphical representations menu,
> and use the "draw multiple frames" input box to specify "0:60" or
> whatever the number of symmetric units in the structure are.
>
> If you prefer to have VMD build a complete structure from the
> complete biological unit file from the PDB, you can use the
> "mergemultiframepdb" script in the VMD script library:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mergemultiframepdb/
>
> Let us know if you need more help with this.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Oct 31, 2006 at 01:22:19PM -0500, Adrian Kaats wrote:
> > Hi,
> >
> > I have read the posts concerning the use of mono2poly.tcl to create biological unit coordiante files, and it works great in most cases. Unfortunately, there are some PDB files that do not seem to contain appropriate instructions for creating the biological unit and therefore do not work with mono2poly.tcl (example Ompf Porin 2OMF from RCSB). However, RCSB does provide a .pdb containing the coordinates for the biological unit - this file can be downloaded by clicking on 'Biological Unit Coordinates' under 'Download Files' on the left panel of the structure viewer.
> >
> > MY PROBLEM:
> >
> > When I load the 'Biological Unit Coordinates' file in VMD I can't get it to show the entire unit - it will only show the assymetric unit (please try this with the biological unit coordinates file for Ompf). It should be noted that both Rasmol and KiNG will display the entire biological unit, so there is nothing wrong with the coordinates file.
> >
> > Does anybody know how to get VMD to display the entire biological unit?
> >
> > Thanks,
> >
> > Adrian Kaats
> >
> > Graduate student
> > Department of Biomedical Engineering
> > McGill University
> > Montreal, Quebec
> > Canada
> >
> >
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> --
> 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
>
>
>
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-- 
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