[Chimera-users] [ViewDock] wrong bonds

Aurelien GROSDIDIER agrosdidier_phd at yahoo.fr
Mon Aug 29 02:36:31 PDT 2005

Hi all !

I'm currently trying to use the ViewDock plugin to visualize results coming 
from our in house docking program, which dumps PDB files. These PDBs are them 
transformed into in a DOCK3/DOCK4 compliant format. First, I should say I 
haven't seen a clear description of this format, and the script gathering 
together PDB files is very empirical. The problem I see might come from a 
mistake of our docking program. Urls to fock3/4 specifications are thus 
welcome :)

Problem context:
The problem happens when dealing with ligands having several distinct residue 
numbers or if the docking coordinates do not consist only of a ligand, but 
also a set of sidechains of its receptor (also with distinct residue number).

Problem symptoms:
The representation loaded using ViewDock show bonds between each and every 
atoms of the ligand (and the sidechains, if any), no matters their atom type 
or how far they are. This is kinda of weird, as the representation is perfect 
when these PDB are loaded from individual PDB files (not using ViewDock).

I am a newbie on this mailing list, and unfortunately this problem should be 
solved withing a few days or so. I would like to apologize in advance in case 
this help request should go somewhere else. And in case you need a clearer 
description of the problem (with figures, input files and so on), feel free 
to contact me either directly or using the ML :)

Thanks a lot for your help,

Aurélien Grosdidier

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