[chimera-dev] RMSD map, urgent help please

[Eric Pettersen]

On Jun 22, 2011, at 3:51 AM, Jean Didier Pie Marechal wrote:

> Hi guys,
>
> Sorry to ask you that but I urgently need to recover the matrix from  
> an RMSD map obtained from a MD movie. Basically, that would be the  
> same as the graphic of the map but in a file with the numbers. I  
> only have 40 structures but doint it by hands is just painful. Could  
> you please tell me how to catch the rmsd map, I guess we can do it  
> from the script section of the MD movie, but can't figure it out.

Hi JD,
	I guess the simplest way is just to insert a print statement where  
the RMSDs are being computed.  In the Movie module there is a file  
named RmsdMap.py that you can edit.  Line 232 of that file should look  
like this:

				self.rects[rect1] = (frame1, frame2, rmsd)

add a print statement right after that, with the same indentation,  
like so:

				print frame1, frame2, rmsd

Then all the computed RMSDs and frame numbers will be reported in the  
reply log, from which they could be saved.
	It would also be possible to write a script that fishes around to  
find the RMSD-map dialog and extract the RMSDs.  If you really need  
that instead of the print-statement approach let me know and I'll whip  
up something.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

On Linux/Windows, the Movie module is in <your Chimera installation>/ 
share.  On Mac, it's in Chimera.app/Contents/Resources/share.