[Chimera-users] DockPrep sometimes fails with altPos

Visvaldas Kairys visvaldaskairys at gmail.com
Mon Jun 12 01:57:26 PDT 2017

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,


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