ADL: Discrepancy in results by different Viewers

Garrett M. Morris garrett at
Mon Jan 7 18:05:32 PST 2008

Dear Anurag,

On Wed, 26 Dec 2007, ANURAG BAGARIA wrote:

> Dear Members / visitors of this mailing list,
> I have noticed a peculiar problem while viewing the protein or ligand files
> using different viewers.
> The same ligand or protein (same file) when viewed in one viewer appears to
> be broken, distorted while in a different viewer it appears intact and fine.
> I have come observed this while using different viewers such as Pymol, ADT,
> VMD, and Viewerlite (from Accelreys).

I suspect this may be caused by the re-ordering of atoms that occurs 
when a PDBQ/PDBQT file is written.  Many viewers assume the order of 
the atoms in amino acids will follow some standard template.  The 
solution would be either to restore the original order of atoms, or 
use CONECT records if using a PDB file format.  If you have a problem 
with ADT, please let us know so we can fix it.

> It would be grateful if someone could explain the above phenomenon, which
> sometimes leads to wrong interpretation of results.
> Hopeful of a positive response from the members.
> Warm regards.

I hope this helps,


Dr Garrett M. Morris, MA, DPhil

The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: garrett at
La Jolla,  CA 92037-1000,  USA.

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