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

[compchem compchems]

Dear Elaine, thank you very much for your detailed response on my somewhat careless apply. It's your very kindly and useful help for me. I just thought about letter size and as it turned out missed the important issues. I am sorry for.

First, I use two-stage Chimera procedure (MatchMaker and then Match->align) for multiple sequence alignment with the spatial superposition for detailed analysis of variable ligand binding (or, in some cases, non-binding) site in my enzymes (with full sequnces lengths available in 3D structure in analysis, not in sites, of course).

Second, I think I understand MatchMaker procedure, parameters and detailed analysis on these subject in your and co-wokers article "Tools for integrated sequence-structure analysis with UCSF Chimera". Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. BMC Bioinformatics. 2006 Jul 12;7:339. PMID: 16836757. Especially about robustness of algorithm for broad range of parameters and even for search scheme (local SW or global NW). This article is wery informative for me. So, I used here default parameters and omit this step in my first appeal.

Third, in my first original question I mean not cut-off value, while you answer drew my attention on rationale on this subject (thank!), but on how choice between "at least one other" and "all other" in 
"Residue aligned in column if within cutoff of" parameter may influence on final result with my set (how robust algorithm for such a choice).

Fourth, about my second original question in the light of the goal described above. How choice of "Superimpose full column" between "entire alignment" and "in stretches of at least N the consequtive columns" may change results for my set. Or, perhaps, in my case default parameters will be ok?

Fifth, great thanks for material about quality assessment.

With my best wishes to you, Dmitry Yegorov.