[Chimera-users] Chimera - Matchmaker tool

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 28 09:47:33 PDT 2008

On Apr 27, 2008, at 10:16 AM, Sujata wrote:

> Hi,
> I am using Chimera for awhile now to analysis modeled structures  
> and I love it, way better for visualizing than a lot of other  
> softwares and very user freindly.
> I do have a question about Matchmaker- is there a way that I can  
> get the total number of atom-pairs in the 'matchlist' it generates  
> in Matchmaker? Or in other words, I want to know the final  
> percentage of atom-pairs that Chimera gives me after pruning the  
> long atom pairs that do not exceed 2 Angstroms to compute the RMSD.
> Thank you very much.
> Sujata Sovani

Hi Sujata,
Thanks, tell your friends!  8-)

The final match RMSD and number of alpha-carbon pairs are reported in  
the Reply Log (under Favorites).  They are also shown in the status  
line at the bottom of the Chimera window, but only temporarily.  If  
you also show the sequence alignment from MatchMaker, these residue  
pairs used in the final fit iteration are shown in boxes with orange- 
red outline and light orange interior.

I am not sure which percentage you wanted; one possibility is to  
divide by the total number of residues in a structure.  You can also  
find out how many pairs were pruned by doing another match with the  
same parameters except without iteration.  That does not change the  
sequence alignment, only the fitting.  If you already showed the  
sequence alignment from matchmaker, you wouldn't have to rerun  
matchmaker, only choose Structure... Match from the sequence  
alignment window and apply it with all its options turned off.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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