[Chimera-users] Find Clashes/Contact (or FindHBond) after splitting chains?

Mark Girvin mark.girvin at einstein.yu.edu
Fri Sep 19 11:21:59 PDT 2014


A student in our Biochem class (we have them use Chimera, and tell them that this choice is because it is such a well-done program, and has such active support from the developers and mailing list -- thank you all!) was trying to use Tools->Structure Analysis->Find Contacts/Clashes (and FindHBonds, with the same problem) after running split to simplify displaying and hiding the 14 chains in the  coordinate file of the oligomer (1avo) that he was working on.

Selecting the residues in one chain (now one model), designating them as the first set within Find Clash/Contacts, checking against all other atoms, choosing "contacts" and applying (Find Contacts) gives no contacts (0 contacts on Reply log). But if run before splitting (selecting chain A and running Find Clash/Contact with the same settings) finds many contacts. The same holds true when using FindHBond - works pre-split, but not post-split.

I was wondering whether we were doing something wrong, or if this is the expected behaviour?


 - Mark

(our work-around was to delete different subsets of chains and save the resulting coordinates as "HeteroDimerDimer.pdb" &  "HeteroDimer.pdb" and then work with those, which went fine)

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