[Chimera-users] Ca-Ca difference plot

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 30 13:38:24 PST 2016


If you really did want to compare the conformations with RR distance maps, however, superimposing the structures is not necessary since only the intra-structure distances are involved.  You would just start RR Distance Maps, choose both structures in the “Chains” area of the dialog,  choose the “Difference” option and then click “Calculate Map.”

Then you can see intra-protein distances that are longer in one structure as one color and intra-protein distances that are longer in the other structure as the other color.  The “Export…” button allows writing out values to plot in some other program.

For example, here is an RRDistMaps “Distances” plot comparing 2fw0 and 2gbp:



Here is the result from what I described in the previous email message, CA-CA distance histogram (“RMSD:ca”) for 2gbp and 2fw0 after they were superimposed with MatchMaker.




> On Nov 30, 2016, at 1:24 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Luca,
> RR distance plots show intra-protein distances, between pairs of residues in the same structure (although they can be compared amongst different structures).
> 
> It sounds like you want a plot of the distances between the same (or corresponding) residues in two different proteins.  Iif they have the same sequence or similar sequences, you can just associate both structures with either sequence. Then CA RMSD can be shown as a histogram over the sequence and the values can be saved, or shown with color, worm fatness, etc. If there are only two structures, the CA RMSD is simply the CA-CA distance between them.
> 
> (1) open both structures, superimpose them however you like (many ways in Chimera)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> 
> (2) show sequence of either one, doesn’t matter which (menu: Favorites… Sequence)
> 
> (3) associate both structures with that sequence using sequence-window menu: Structures… Associations
> 
> (4) show CA RMSD histogram above sequence using sequence-window menu: Headers… RMSD: ca.  That is the only plot of these values directly available in Chimera, but you can write out the values as described below and use some other plotting method.
> 
> (5) with the Render by Attribute tool (in menu under Tools… Depiction), you can show the residue-attribute “mavRMSDca” values with color and/or worms on either structure, or write out values with its menu: File… Save Attributes
> 
> 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 30, 2016, at 10:49 AM, Luca Pellegrini <lp212 at cam.ac.uk> wrote:
>> 
>> Hi,
>> I have superimposed two structures of the same protein in two different conformations, and now I would like to calculate a plot of the distances between alpha carbons for each residue in the two conformations, to quantify the relative movement of different domains in the protein structure. Can anyone please explain a simple way of doing this in Chimera?  Apologies if I missed something obvious, I tried 'RR distance maps' but couldn’t figure out how to do this simple task. 
>> 
>> Best regards,
>> Luca
>> 
> 
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