[Chimera-users] Question about match

Ibrahim Moustafa I.moustafa at psu.edu
Mon Jul 26 14:16:44 PDT 2010

Dear Chimera developers,

 I have a question related to the ³match² command.
I wanted to align 4 related proteins and I used the default in the match
The alignment is fine; but I have a question about the output in the reply
In the log it says:
 ³evaluating superpositions across all 439 fully populated columns in the
final alignment²
 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?
I¹m 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,

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