[Chimera-users] Analysis of the multiple alignments + structures

Dear Chimera Users! I'd like to perform analysis of the set of the sequences (presented in the FASTA multiple-alignment file) together with the some (not all) X-ray structures available for several of the sequences presented in its database to detect conservative motifs (from sequence) and make conclusions about its functional importance (based on the analysis of the Xray data) to make conclusions between conservation of sequence and it's functional relevance. Could you provide me with the some useful Chimera plugging as well as for some tutorials Kind regards, James