VMD-L Mailing List
From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Jan 20 2015 - 23:15:12 CST
I'd been wondering about this for a while, and finally tracked it down...
On line 2667 of autopsf.tcl (in the VMD 1.9.2 release) there is the line:
set sel2 [atomselect $currentMol "(not resid $resid) and resname CYS and name SG and index > $index and exwithin 3.0 of index $index"]
This should read:
set sel2 [atomselect $currentMol "resname CYS and name SG and index > $index and exwithin 3.0 of index $index"]
At present, it skips disulfide bonds between cysteine residues which are on different chains but happen to have the same resID. This crops up surprisingly often (e.g. insulin, which disulfide bonds between CysA7 and CysB7).