VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 16 2004 - 17:25:36 CST

Hi,
  I've written a script to merge these Virus capsid PDB files which are
stored as multi-frame PDB files into single structures within VMD using
a some relatively simple VMD and 'psfgen' scripting. This script has been
tested with one of the Virus capsids on the PDB site and it worked ok so far,
give it a try and let me know if you have any trouble using it.
  ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/k4/1k4r.pdb1.gz

Just as a warning, the resulting structure file contained about 1 million
atoms, so be careful that you've got enough memory in your computer before
you start getting carried away with this stuff :-)

I've attached the script to this email.

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 13, 2004 at 09:50:30AM +0900, piriboy wrote:
> Dear
>
> 1. Some pdb file which contains protein multimer, e.g. virus capsid
> might be generated by PDB matrices, is loaded in multi-frames in VMD.
> Can I load all of those in a frame??
>
> 2. The surface model which was generated by MSMS looks very nice,
> fantastic and smooth in VMD OpenGL window. But, when this scene was
> rendered with ray-tracing program like POVray, the interface between two
> different colors triangles look zig-zag, not smooth. Any idea??
>
> Thanks
>
> DongHoon Chung
> Korea University. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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