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

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 19 13:06:17 PDT 2014

Hi Mark,
Thanks for the kind words… we try!

The behavior is because:
(1) “split" makes submodels with the same main model number, which are otherwise mainly encountered for molecules you don’t really want to see each other, like members of an NMR ensemble or different poses of docked ligands

(2) thus the FindHBond and Find Clashes/Contacts GUIs automatically suppress all interactions between submodels with the same main model number

For more advanced usage, the “findhbond” and “findclash” commands do allow turning this off by using option “interSubmodel true”.  So far we didn’t put such an option in the GUIs because they are already quite complicated.  Command docs:

Other than using the commands, I’m not sure what the best workaround would be.  Each adds steps and thus inconvenience.  Your workaround worked because when you open the files, they have different main model numbers.  You could also split and then save/reopen the structures with the same effect, as long as you saved them to separate files instead of one multi-model file.  

You could circumvent writing/reading extra files by splitting and then copying a submodel to create a new model with a different model number.  This can be done with the “copy/combine” function in the Model Panel or the command “combine" (we already had a “copy” command that does something else).  You’d probably want to close the original copy, the submodel, to avoid later confusion.

I assume you would still rather use “split”; of course, not splitting is another possibility.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 19, 2014, at 12:36 PM, Mark Girvin <mark.girvin at einstein.yu.edu> wrote:

> (Apologies if this arrives twice - on rechecking it, the email address that I tried first looked wrong)
> Hello,
> 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?
> Thanks,
> - 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)
> - Mark

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