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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users