[Chimera-users] ViewDock: flexible receptor residues in different chains

Conrad Huang conrad at cgl.ucsf.edu
Fri Mar 8 13:19:10 PST 2013


This should be fixed in tomorrow's daily build (anything dated March 9 
or later).  ViewDock will reads chain identifier and insertion code 
along with residue sequence.  Consecutive residues with different chain 
identifiers will not have a bond between them.  The only thing I'm not 
sure about are the missing bonds.  Can you please take a look and see if 
there are still missing bonds in the new version?  Thanks.

Conrad

On 3/6/2013 8:27 AM, Jérôme Hénin wrote:
> Hi everyone,
>
> When viewing Autodock Vina results in ViewDock, I hit a problem that
> I think is due to insufficient parsing of the PDBQT file. I have
> flexible receptor residues in two identical chains, say, Leu15 in
> chain A and Leu15 in chain B - these sidechains are part of the PDBQT
> file. However, ViewDock apparently ignores chain identifiers in that
> file, so it is unable to distinguish between these two residues, and
> it creates mangled bonds linking them while some other bonds are
> missing.
>
> I don't know how much work it would be to parse chain identifiers
> from the PDBQT file, I would have a go at it if I was more of a
> Python person, but I really am not.
>
> Best, Jerome _______________________________________________
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