VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 21 2009 - 16:50:06 CDT

Hi,
  For 1) I would assume that the normal "measure fit ..." commands
shown in the VMD tutorials should work fine, so long as you pick matching
particles for your two CG structures. If the order of the particles is
different, then you have to provide an index map parameter as well.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 21, 2009 at 06:56:24PM +0200, Umesh Ghoshdastider wrote:
> Hi there,
>
> I recently started using vmd and having hard time solving following problems:
>
> 1. How can I align or superimpose two CG protein structures? I can't
> do it in other software since it is CG and I had to write a script so
> that vmd connects and colors the grains of the protein which other
> softwares don't understand. Just manually moving molecules by mouse
> does not work.
>
> 2. How can I count no. of other molecules (say resname abc) around the
> given distance from the protein over time? Is it possible to color
> those molecules, given the distance from the protein?
>
> Thanks a lot for your trouble.
>
> Best regards,
> Umesh 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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