[Chimera-users] Calculate RMSD over SSE of NMR ensemble

[Eric Pettersen]

Aside from the fact that I should probably make it easier to get an entire ensemble associated with a member's sequence, one further thing to note that if you bring up the Region Browser (from MAV's "Info" menu) then it will also show the RMSD value for any regions on the alignment -- in particular since there is a region for all the strands and another for all the helices, it will show the RMSD across all stands together, and across all helices together, if that is of interest to you.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jul 10, 2014, at 5:39 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Markus,
> 
>   There is no special function to compute RMSD of each secondary structure element in an NMR ensemble.  But it is pretty easy to do.  Open the NMR ensemble and display the sequence of the first structure (menu Tools / Sequence / Sequence).  Now the ugly part.  You need all your structures “associated” with the shown sequence, so use the Sequence dialog menu Structure / Associations… and set every structure in the NMR ensemble to be associated with the sequence.  This involves clicking a separate check button (associate with best match) for each of the structures and is a real pain for 25 structures.  Maybe there is a better way of doing it that Chimera sequence experts Elaine and Eric would know.  Once you do that if you drag a box in the sequence window around an alpha helix (each helix is shown as yellow in the sequence) then it reports the RMSD (CA atoms all pairwise distances treated equally) for the selected helix.  These are also reported in the Chimera reply log (menu Favorites / Reply Log).  Even if you were willing to type the residue ranges for each secondary structure element, I don’t know of a Chimera command that will do it since the “rmsd” command only takes 2 structures at a time.  Would be nice if something like "rmsd #0:51-60 at CA ensemble true” would compute the RMSD for those residues for all the members of NMR ensemble #0, but we don’t currently support that.
> 
>   One more thing to note — the sequence dialog RMSD calculation is not RMSD of all ensemble members to an average structure.  Instead it looks at all pairwise distances between matched atoms in the N structures (so N*(N-1)/2 pairs) and averages those.  An RMSD to an average structure would be smaller.
> 
>   A related question of finding per-residue RMSD values within an NMR ensemble was answered earlier
> 
> 	http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009526.html
> 
>     Tom
> 
> 
> On Jul 10, 2014, at 2:29 PM, Markus Heller <mheller at cdrd.ca> wrote:
> 
>> Hello,
>>  
>> The subject says it all.  How do I calculate the RMSD of secondary structure elements of an NMR ensemble?  I did RTFM, but I’m hoping that I can avoid spelling out the residues comprising the SSEs …
>>  
>> Thanks and Cheers
>> Markus
>>  
>> --
>> Markus Heller, Ph.D.
>> NMR Scientist
>> CDRD - The Centre for Drug Research and Development
>> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147
>> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller at cdrd.ca | www.cdrd.ca
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