VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 24 2009 - 16:40:44 CDT

Hi,
  What program are you loading the resulting PDB file into?
I will change the PDB writer to avoid the problem you
mention below. It shouldn't be changing the numbering scheme mid-way
through writing the file, that's an unintended side effect of the way
the routine that emits the atom records is being called. I'll see
if I can address that.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 24, 2009 at 04:51:54PM -0400, Jianhui Tian wrote:
> Hi,
> I am currently using the vmd 1.8.6 version. I have a system of more than
> 9999 residues(or 99999 atoms). If I want to save the configuration in PDB
> format after loading into vmd, the residue index is first base on the
> decimal index from 1, 2, 3, ..., 9999. When there are more residues than
> 9999, the residue index larger than 9999 will be converted to hexadecimal
> number. This introduces a problem: there will be two different residues
> with the same residue index (for example 1234), one is decimal based while
> the other is hexadecimal based. How can I use the residue index to
> identify residue uniquely? Thanks.
> Jianhui 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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