[Chimera-users] structural alignment

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 6 16:11:59 PDT 2010

Hi Bala,
You can repeat the whole process as described for each principal chain, but the RMSDs would be for the chains superimposed separately rather than both at the same time.  Or, you could just strip out the TERs and pretend each model with two chains is a single chain, to perform the process on both together.

I am not sure what a box plot is, but besides showing RMSDs with color or worms on the structure, you could
(a) save the sequence window contents, which includes the RMSD header histogram, as an EPS file (see File... Save EPS in the sequence window menu).
(b) save the mavRMSD values to a text file using Render by Attribute (see File... Save Attributes in that dialog).  Then you could convert that file as needed to make input for some other plotting program that is able to make the kind of plot you want.
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 3:59 PM, Bala subramanian wrote:

> Dear Elaine,
> Thank you. But i have a problem in doing this because my RNA has two principal chains [two strands seperated by TER card, attached pdb file]. It would be nice if there is a way to output the rmsd so that i can make a box plot to show which residues are flexible among those conformations.
> Thank you,
> Bala

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