I want to simplify the question I asked yesterday. Is there any way to store the output of Match Maker, specifically the RMSD values for every residue and the list of residues in the alignment regions in an external file from command line?

Hello, I just wanted to bring up a related issue: the sequence alignment you get from MatchMaker is not a fully structure-based alignment. If the sequences are fairly easy to align, this is not an issue, but when sequence identity is low, you may want to generate a structure-based sequence alignment with Match->Align after superimposing the structures with MatchMaker. More explanation... by default, MatchMaker: (1) generates a pairwise sequence alignment using standard methods. Some structure information is used at this step because the alignment score includes both residue type (alanine, arginine, ...) and secondary structure (helix, strand ...). (2) uses the sequence alignment to fit the structures. At first all columns are used, but iterating the fit discards the columns where the structures match poorly in space. If there are sections of the alignment that are wrong, the iteration process tends to exclude them from fitting, resulting in a good-looking superposition. Therefore, a successful and correct superposition (as determined by eye) does not mean all the parts of the sequence alignment are right. If the sequences are similar enough that you don't think errors in the MatchMaker sequence alignment are an issue, saving the residue pairing and RMSD header (which for pairwise is simply the CA-CA distance) directly from that alignment is fine. If you are getting into the twilight zone of sequence similarity, I suggest running Match->Align on the superposition, then proceeding with that second sequence alignment instead. Another advantage of Match->Align is that it can make a single sequence alignment of >2 superimposed structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchali...

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmak...

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