Hi Elaine, Thanks for your reply. Yes, I used the match->align tool. That is what I wanted to know. Many thanks, Ibrahim -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, July 26, 2010 5:26 PM To: Ibrahim Moustafa Cc: Chimera BB Subject: Re: [Chimera-users] Question about match Dear Ibrahim, I am guessing you are using the "Match->Align" tool. (The match command is somewhat different). The 439 mentioned in the log is the number of fully populated columns in the multiple sequence alignment (columns with 1 residue from each structure, no gap characters), so 439 CA atoms in each structure are used. Each pairwise RMSD describes how 439 CA atoms from one structure are superimposed on 439 CA atoms from the other structure. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 26, 2010, at 2:16 PM, Ibrahim Moustafa wrote:

Dear Chimera developers,

I have a question related to the "match" command. I wanted to align 4 related proteins and I used the default in the match menu. The alignment is fine; but I have a question about the output in the reply log. In the log it says: "evaluating superpositions across all 439 fully populated columns in the final alignment" Then the pair-wise RMSD between the different pairs (range from 0.7 - 1.6 A) are given.

What is meant by 439 fully populated columns? Does it mean 439 C-alpha atoms for those amino acids in the fully occupied aligned columns? I'm asking because I want to report these values of RMSD and I want to be more specific and state the number of atoms over which the RMSD value is being reported.

P.S. The proteins vary in their length (461,462,460 and 470).

Thanks for your reply in advance,

Ibrahim