VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 13 2004 - 11:31:34 CST

Hi,
  Here's my current suggestion for these questions:
1) At present VMD always loads multi-frame PDB files as a trajectory.
   While I plan on implementing an alternate behavior to load them as
   separate molecules (useful for people doing NMR stuff), this still
   doesn't address the specific use-case you're asking about. To handle
   the type of file you're asking about, the best solution would be to
   use a script to merge all of the structures into a single molecule.
   I ought to be able to provide such a script in the near future since
   a couple other people have asked about this recently.

2) I have a fix for this in the new VMD 1.8.3 test versions, which gives
   greatly improved results when using Tachyon. We're still working on
   improving the output of the other renderers to match. I'll post the
   latest test version later today if all goes well.

Thanks,
  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
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