[Chimera-users] structural similarity measures in Chimera

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 31 13:03:14 PDT 2010

On Mar 30, 2010, at 9:04 PM, Elaine Meng wrote:

> However, there are some issues that may affect whether you decide to  
> use Chimera to calculate these values for your structures:
> (1) You would need to run Match->Align for each pair.  There is no  
> option to do all pairwise comparisons on multiple structures.  You  
> would need to script looping through all pairs (with python or shell  
> scripting).
> (2) There is no Chimera command for Match->Align.  Thus Match->Align  
> would also need to be run via python. I don't have scripting  
> expertise, so someone else would have to provide more details if you  
> decide to try this.

Given that you said you wanted a complete pairwise matrix of ~50  
structures, that would be ~1200 unique pairs, which is obviously way  
too many to do by hand.  Currently Match->Align is awkward to script,  
even in Python, since all the important code is internal to the Match- 
 >Align dialog and basically impossible to call externally.  If you  
are sure that you would like to use Chimera for this computation I can  
reorganize the Match->Align code so that it could be called  
externally.  I don't think the reorganization will be difficult.  You  
would still need to resort to a Python script to make the Match->Align  
calls and loop through your models, so you would need some rudimentary  
familiarity with Python.  Let me know.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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