VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 27 2003 - 22:51:57 CST

Dear Randall,
  There's no easy way to do this in VMD 1.8, however we have a new
feature in VMD 1.8.1 which will make it possible for you to color structures
by time-varying user data fields. If you would like to test the new
VMD 1.8.1 we can tell you how to do this. In either case, there's no way
to do it directly via the occupancy field in multi-structure PDB files.
At present, VMD treats additional PDB structures as additional
coordinate sets, but does not store all of the other fields with each
coordinate set, as you noticed, it uses the data from the first PDB
structure for all of the rest of them. Eventually we'll teach VMD
to store more data on a time-varying basis, but at present we don't
have that built-into the existing file readers etc. For now, Tcl commands
in VMD 1.8.1 will allow you to try this out.

Let us know if you want to try a test version.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 27, 2003 at 12:37:35PM -0600, Randall Hall wrote:
> Hello, I am trying to visualize a simulation in which i use the OCC field
> of a pdb file to color code the atoms. The color coding is to change from
> one frame to another in the animation. I read in the molecule and use the
> occ to color the atoms and all is fine for the first frame. the second
> frame, however, appears to retain the OCC info from the first frame, as the
> colors do not change. i have used the color panel to move the midpoints,
> etc. for coloring and still no change. does vmd only use the first frame to
> get the OCC info? If so, can I accomplish what I want to do using some
> trick?
> a sample file is below:
>
> COMPNDGlass 256 -4.3686097
> AUTHOR R Hall
> ATOM 1 Ar 1 -4.500 4.760 -5.446 0.33 3.40
> ATOM 2 Ar 2 -7.753 -4.286 -7.383 0.94 2.30
> END
> COMPNDGlass 256 -9.7700695
> AUTHOR R Hall
> ATOM 1 Ar 1 -4.610 5.007 -5.649 0.91 2.40
> ATOM 2 Ar 2 -8.060 -4.577 -7.967 0.12 2.90
> END
>
>
>
>
> Randall W. Hall
> Professor of Chemistry
> Department of Chemistry
> Louisiana State University
> Baton Rouge, La. 70808-1804
> rhall_at_lsu.edu
> 225-578-3472 (voice); 225-578-3458
> (fax);http://chem100a-9.chem.lsu.edu/chem/facultypages/hall/hall.asp 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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