On 4/7/11 8:26 AM, Benjamin SCHWARZ wrote:
As a first (naive) question on that mailing list, I wonder if (and how) it is possible to retrieve residues that are structurally aligned as a result of a aln.salign() run (object aln being of type alignment). To precise my question, I know a (multiple) sequence alignment is produced as a result of this salign command and can be output with aln.write(), but I am more concerned by the possible mapping of residues in the structural alignment, that might not be apparent in the sequence.
Modeller does not make use of such a mapping internally. If two residues are aligned, then SALIGN uses the Cartesian distance between those two residues as an alignment score (put simply). It will modify that alignment to optimize that score. There is no difference between two residues being aligned "sequentially" or "structurally".
Ben Webb, Modeller Caretaker
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