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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html