Re: solvate

From: Brian Bennion (
Date: Mon Nov 03 2003 - 11:27:56 CST

Hello Himanshu

VMD keeps the chain id column the way it was when it read in the file,
unless the format is slightly off, which appears to be the case for your
file. The extreme right column is not the pdb chain id column it is the
NAMD segment column and only means anything in NAMD or VMD from what I can

If you could send your pdbfile that was generated in solvate I can take a
look at it to better understand your questions.


On Sun, 2 Nov 2003, himanshu chandola wrote:

> hello everyone,
> running solvate to put a waterbox ultimately gives a pdb file
> which has the chain name on the extreme right column instead of the usual
> column. Now due to this vmd names every chain as X. Now if i just wish to
> display my molecule itself which has A,B,C,D and E chains - i can't do
> that -- i can only have the molecule with a waterbox .
> Anybody has idea about anything which i might be missing,
> thanks in advance,
> himanshu
> ======================
> himanshu chandola
> iit delhi
> ----------------------------------------
> Morpheus: Do you believe in fate, Neo?
> Neo: No.
> Morpheus: Why Not?
> Neo: Because I don't like the idea that I'm not in control of my life.

**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **

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