[Chimera-users] Troubleshooting Residue Errors

Eric Pettersen pett at cgl.ucsf.edu
Fri Jul 15 10:57:24 PDT 2016


Well, this is a bug with Chimera, but would be a lot of work to fix.  There are alt locs throughout this structure and Dock Prep decides on which alt loc to keep on a per residue basis.  This is a problem in the rare structure like this where there are alt loc positions for backbone atoms, not just side chains -- so in a few cases in adjacent residues it picks different alt locs, which causes the residues to lose covalent connectivity and therefore spurious HNs get added.  The solution for you is to delete unwanted alt locs before running Dock Prep, then everything will work.  For instance, to remove the B and C alt locs (leaving A), use this command:

	del @.B @.C

(Favorites->Command Line to show the command line).

ChimeraX handles alt locs in a completely different manner and this issue will be moot then.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jul 15, 2016, at 9:40 AM, Mike Bergman <bergm310 at umn.edu> wrote:
> 
> Good Morning.
> I am trying to Dock Prep the kappa1 dimer (PDB ID: 2Q20) in order to
> run Molecular Dynamics simulation.
> I keep getting an error that I'm not sure how to solve.
> I cleared the reply log and tried again so I could attach the reply
> log to this email.
> I have not modified the structure at all prior to the dock prep.
> 
> When I looked at the residues, they seemed fine to me, but maybe you
> can help me figure out what's wrong.
> Any help would be appreciated.
> 
> Thank you very much.
> 
> Sincerely,
> Mikey Bergman
> <Residue>_______________________________________________
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