Dear Chimera Help,

I have used NCBI’s COBALT to align the active site residues for the ~400 kinases in the ‘kinome tree’. This fasta alignment can be exported and read into chimera. 

Once loaded,

tools  >  sequence  >  multialign/viewer > info > percent identity

gives me the % identity for a pair of sequences. Since I have ~400 sequences, I would like to know whether the upper-triangular matrix of percent identities can be done automatically. If so, can a weight matrix for scoring (BLOSUM62) be used?

Thanks in advance for your help.

David Covell, Ph.D.