[Chimera-users] rmsd calculation for pre aligned structures

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 2 15:17:49 PST 2015

Hi Oliver,
In that case, you can just show the sequence of one protein, then use the sequence window menu: Structure… Associations to associate both structures with that one sequence, then sequence window Headers menu to show the RMSD of interest, etc.

This would work even if the sequences of the structures were slightly different, as long as they were both similar enough to the sequence in Multalign Viewer that Chimera could figure out the association accurately.

On Mar 2, 2015, at 3:12 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi Elaine, thanks for the reply! This sounds like exactly the right solution. However, when I try to add a sequence in the sequence dialog, Chimera hangs on “running Needleman-Wunsch”. 
> I suspect this is because my sequences are so long (~5000 residues). 
> But I don’t actually need to align them - they are already aligned as they are actually the same sequence, because I am looking at different conformations of the same protein. 
> I guess I can create a dummy sequence alignment, with two identical sequences, but it would be nice to have some way of telling chimera not to align the sequences, or to allow for manual alignment in cases such as these - perhaps a “Do not align” or “align manually” checkbox in the add sequence dialog would do the trick.
> Thanks again,
> Oliver.

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