[Chimera-users] Parameters choice for match->align and quality assessment

[compchem compchems]

Dear Chimera developers, great thanks to you for possibility to work with your very useful program.

I am new in structural alignment studies and have some questions about parameters in match->align.

My set cosists of few closely related proteins with same function and conservative spatial structure, but with some divergence in aminoacid sequences except of conservative functional residues.

First, what "Residue aligned in column if within cutoff of" influences on and what preferable choice may be in my case.

Second, "Superimpose full column" - how can i decide what to select for my set or what play can help me.

Third, how can i evaluate quality or correctness of obtained alignment (may be, common procedure).

I am sorry for long letter and thanks for your attention to my problem.

D. Yegorov.