-chainmap -- Question/docs enhancement proposal

[ulupo]

Hi,

Thanks for the great tool!

I have a quick question about the -chainmap option, that could perhaps lead to an improvement in the docs. Namely: is the custom chain mapping here supposed to be "complete" (given the other options passed by the user)? Or, is the program going to accept partial chain mappings that act as constraints on the set of all possible chain permutations? E.g., if the user decides a priori that map A in PDB file 1 should only ever be mapped to map A' in PDB file 2, no matter the TM-score, while chains B, C, ... from PDB file 1 can be mapped arbitrarily to chains B', C', ... from PDB file 2.

Thank you in advance for the clarification!