[Chimera-users] Chimera scripting question

Oliver Clarke olibclarke at gmail.com
Mon Sep 25 12:18:45 PDT 2017


Hi,

I’d like to do the following (presumably with a python script):

For each pair of Calphas in two identical structures A and B:
	Get list of other Calphas within distance cutoff of Calpha(0) for each conformation (say 10 Å);
	For each Calpha in list:
		Calc distance difference diff_dist between Calpha(0—>A), Calpha(0—>B)	
	average(diff_dist) over list and assign to attribute

So more or less, I think I need to 

(1) iterate through all Calphas of the first structure (this part I get); 

(2) check if there is an equivalent Calpha in the second structure (same residue number and chain I guess?); 

(3) get a list of nearby Calphas, merged between structures (not exactly sure about this but I think I found something in an example I can adapt) 

(4) calculate distances, then difference-distances between the paired structures, from each target Calpha;

(5) assign the averaged difference distance to an attribute (I think I can figure out this bit)

Any suggestions much appreciated (or if anyone can point me towards similar scripts I can adapt the would also be most welcome!)

The intent of this is to generate an attribute representing local structural flexibility (independent of displacement) - to capture changes in the local arrangements of atoms, decoupled from rigid displacements of domains. The idea is this may be useful for highlighting hinge regions and regions that have undergone plastic deformation, without pre-aligning structures.

Cheers
Oli





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