[Chimera-users] DockPrep sometimes fails with altPos

Eric Pettersen pett at cgl.ucsf.edu
Tue Jun 13 15:49:24 PDT 2017

Yes, the altlocs are chosen on a per-residue basis, which can lead to inconsistencies when different altlocs are chosen for connected residues (the cross-residue bond(s) gets deleted and hydrogens get added to the now-valence-available atoms).  I will work to fix this when I have time and will report back here when I do.  In the interim, you may want to simply delete non-A altlocs before running DockPrep.  Assuming there are no more than three altlocs per atom then this command will do that:

	del @.b @.c


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jun 12, 2017, at 1:57 AM, Visvaldas Kairys <visvaldaskairys at gmail.com> wrote:
> Dear Chimera users and developers,
> I’d like to point out I often have a minor inconvenience when dealing with high resolution Xray structures when trying to add hydrogens
> via DockPrep. 
> If two consecutive residues have both alternative postions A and B, Chimera in the process of hydrogen addition often gets confused 
> and puts “TER” between the
> residues, also reporting non-integer charges in the log. I think what is happening, the program picks “A” variant for one residue and “B” for the consecutive residue, and apparently this causes bond detection algorithm to ignore the bond between the residues (due to length I guess).
> I resolve this by manually editing out one of the AltPos (say, “B”) out of the PDB file for the offending residues, 
> but I guess the program should be able to do it automatically.
> A PDB example where this happens is 2r3i (or 2r3r).
> Best regards,
> Vis
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