[Chimera-users] All PDB ca atom pairwise distance

Eric Pettersen pett at cgl.ucsf.edu
Tue Oct 31 11:36:27 PDT 2017


> On Oct 31, 2017, at 9:54 AM, Kyle Morris <kylelmorris at berkeley.edu> wrote:
> 
> Dear chimera dev and users,
> 
> Is there a way to calculate (using the GUI, commands or using a python script) the pairwise distances for every single c-alpha atom in a set of loaded PDB coordinates and spit this out to a file for further analysis? There are 142,800 atoms in the current loaded assembly.

Do you mean CA-CA distances, or CA-any-other-atom distances?  Even CA-CA only (assuming CAs are roughly 1/10 of your atoms) will be more than one hundred million distances, and CA-other will be more than a billion.  Is this really what you want?  If so, it would seem more efficient and much faster to write a special purpose program for this in a compiled language, like C, C++ or some such.  It is of course doable in Chimera via Python.  If you really do want to do it that way, I can offer further guidance...

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab





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