[Chimera-users] structural similarity measures in Chimera

Minming Li li362 at purdue.edu
Sat Apr 3 14:09:59 PDT 2010

Dear Dr. Pettersen and Dr. Meng,

Thank you for your last email. I'm sorry that I am not so familiar with
Python, so could you help me to use the Chimera to produce the distance 
matrix of the listed 45 pdbs below? Otherwise, is there any easy way to do this 
just by running the program instead of using the Match->Align by hand? Thank 
you so much! 
The list of the 45 pdbs: 
Best regards!

Minming Li

Minming Li
PhD student,
Interdisciplinary Life Science Program (PULSe Program), 
Purdue University, 
West Lafayette, IN. USA.
Email: li362 at purdue.edu

Quoting Eric Pettersen <pett at cgl.ucsf.edu>:

> 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
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          http://www.cgl.ucsf.edu

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