Modeller users:

When analyzing your alignment file using CHECK_ALIGNMENT, how critical is it to eliminate all of the following errors:

chkaln___> Checking pairwise structural superpositions: Equivalent CA pairs with distance difference larger than 6.0 angstroms:

chkaln___> Checking structure-sequence alignments: Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:

Should you keep refining the alignment until all of these errors are eliminated, or are one or two acceptable (i.e. 6.2 ang., 8.4 ang... )

Nick

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Nick Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada