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

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 6 13:48:49 PDT 2010

Dear Dmitry,
You're welcome.

In Match->Align, "Residue aligned in column if within cutoff of (a) at least one other, or (b) all others", both choices are robust, but it depends what you want.  Imagine that you have three residues X,Y,Z  from three different structures.  It is possible that the CA-CA distance of residues X,Y is less than the cutoff, and of Y,Z is less than the cutoff, but of X,Z is greater than the cutoff.  If you choose "at least one other" then X,Y,Z can all three be placed in one column of the output sequence alignment.  If you choose the more stringent option, "all others," then X,Y,Z cannot all be in the same column of the sequence alignment, and the alignment will be longer and have more gaps.  I usually choose "at least one other" because I prefer a less gappy alignment, but it also depends on what your cutoff is and what you want the columns of the alignment to signify.

This setting will also affect fit iteration because only the alignment columns with residues from all structures (no gaps) will be used in the next cycle of fitting.  If you really only want fitting where each structure is within the cutoff of every other structure, you would choose "all others".

The reason for the "consecutive columns" setting in iteration is that there might be some places where loops from different structures cross or come close to each other, but are not really structurally equivalent.  If you use only columns where adjacent columns are also full (do not contain gaps) it will exclude those isolated positions where loops just happen to cross but are not really structurally equivalent.  Again I would recommend the default, fitting using only the full columns where there are at least three full columns together. 

If you think the results could be improved, then you could try changing parameters and seeing if the scores improve, but definitely try the default values first.  From your description, there is no reason to expect you would need different values.

I hope this helps, and best wishes to you too!
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 6, 2010, at 11:19 AM, compchem compchems wrote:

> 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.
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