On Apr 25, 2008, at 7:32 AM, bala wrote:

Dear chimera friends,

I have a simulated trajectory of a RNA molecule. I want to make a correlation plot based on residue fluctuation. I am new to scritping in python. Can anybody please give me some suggestions or any sample script for such analysis if possible.

Hi Bala,

Is there any particular reason you want to do it in Chimera? It seems that Simulaid (http://atlas.physbio.mssm.edu/~mezei/simulaid/) can do the plotting you're asking about, and it's free to academics.

If there is a particular reason you want to use Chimera, I can provide the programming details related to reading/processing a trajectory. In that case it would be helpful if you could say what format your RNA trajectory is in.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu