[Chimera-users] split ligands and H-bonds

Markus Heller mheller at cdrd.ca
Tue Nov 15 15:57:20 PST 2016


I have a structure of a complex (I tried with several, but here's one example: 3t07).  I want the stick radii for protein and ligand to be different, so I "split ligands" and then set the stick scale in the attributes of the respective model.

When I then try to detect H-bonds between the ligand and the protein, none are found!  They are found, however, when detecting them prior to splitting the model with "split ligands".

I've tried several settings in the Find Hbond dialog:

Find inter-model, intra-model, both: no difference.

Restrict to the models the H-bonds are between: no difference.

Select the ligand and the protein residue participating in the H bonds and using "Only find H bonds with both ends selected": nothing, no H bonds found.

Why is that?

Thanks and Cheers

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