VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 13:33:31 CDT

Hi,
  It turns out that the source of problems here is that since your PDB
written as a single chain, VMD had problems with the bonds between the coils
confusing the structure analyzer. I fixed the PDB file so that they are
two chains by doing these steps, and now it analyzes the structure and
displays it correctly:

set sel [atomselect top "segname A"]
$sel set chain A
set sel [atomselect top "segname B"]
$sel set chain B
set sel [atomselect top all]
$sel writepdb fixed.pdb
mol delete all
mol new fixed.pdb

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 05, 2006 at 01:24:48PM -0400, ivana adamovic wrote:
> Hi all,
>
> I am looking at different graphic representation of long (22474 atoms)
> coiled coil protein (charmm PDB file) and it seems that there are some
> problems. I can't get both segments (chains) using Trace, Ribbons, ...
> It gives me a proper figure for Lines, Bonds, Points, VDW, CPK,
> Licorice representation.
>
> I have never had such a problem before, and it occurs for several
> different versions of VMD (both on PC and Mac) ...
>
> Thanks a lot,
>
> Ivana 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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