[Chimera-users] Chimera -RMSD

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 21 11:35:15 PDT 2010

On Jun 21, 2010, at 6:25 AM, S. Shunmugasundararaj wrote:

> Dear Eric,
> I am using Chimera v1.4. When aligning 2 or more structures, it  
> gives the
> RMSD as a bar graph. Is it possible to get the RMSD value for each  
> residue?
> Thanks
> Raj

Hi Raj,
	I'm guessing the "RMSD as a bar graph" is the RMSD header at the top  
of the Multalign Viewer tool.  You can save the header values to a  
file with the "Headers->Save..." menu entry at the top of the tool.   
This will save the RMSD value for each alignment position to a file.   
This may or may not be useful for you since the residues associated  
with each alignment position aren't indicated in the file.
	Alternatively, each residue involved in the Multalign Viewer RMSD  
header calculation gets a "mavRMSD" attribute assigned to it.  You can  
save these attributes to a file by using the "File->Save  
Attributes..." menu of the Render By Attribute tool (available in the  
Depiction and Structure Analysis tools menus).


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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