[Chimera-users] Percent Identity for specified parts of a structure

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 8 11:39:42 PST 2011

I forgot to mention that by default, MatchMaker will recalculate the secondary structure assignments (we found this to improve some fits by providing more consistency  of helix/strand assignments between different structures).  However, if you want to retain the structures' original assignments, uncheck the option "Compute secondary structure assignments" before using MatchMaker.

On Nov 8, 2011, at 11:07 AM, Elaine Meng wrote:

> Hi Vicky,
> There isn't a command, but there is an option in the menu of Multalign Viewer (the Chimera tool that shows sequences and sequence alignments).   Currently it can only use the entire sequence alignment, but with Chimera you could save and re-open sub-alignments containing just the helix of interest.  It is a little tedious, but at least you wouldn't have to duplicate your structure files.
> You can simply open a sequence alignment file in Chimera, 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment>
> or If you don't yet have a sequence alignment, it can be created in Chimera:
> If you want Chimera to do the fitting/superposition and if the sequences are reasonably easy to align (similar at least in the parts you care about), you could use MatchMaker with "Show pairwise alignments" turned on. 
> If the sequences are not easy to align, and/or you already have the proteins superimposed the way you want and don't want to change that, use Match->Align to create a sequence alignment from the pre-existing superposition.
> These tools are under Tools... Structure Comparison in the menu.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html>
> Then, when you have the overall sequence alignment, you can highlight the part of interest by dragging a box with the mouse, and save just that part with "File... Save as" in the sequence window menu, turning on the option to "Restrict save to active region."  Then open that newly saved shorter alignment in Chimera, and use  its menu item "Tools... Percent Identity."
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#pid>
> You can show the secondary structure assignments on the overall alignment (may help in dragging a box in the right place) with sequence window menu item "Structure... Secondary Structure... show actual"
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Nov 8, 2011, at 7:20 AM, Victoria James wrote:
>> Hi there,
>> I don't know if this command already exists, but I can't seem to find it in the Chimera tools or manual.
>> I'd like to be able to calculate the percent identity of specified parts of 2 matched sequences - in my case the individual transmembrane helices of the structures.
>> I wonder if a command already exists or if there is a way of doing this in Chimera without having to make new .pdb files of each of the areas of the proteins that I want to compare?
>> I think it would be a useful command if it does not already exist.
>> Thanks,
>> Vicky
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