MBG wiki | RecentChanges | Blog | 2021-09-24 | 2021-09-23

Calculation of the average Cα-Cα distance map and the corresponding rmsd

carma it is :

carma -v -rms -mrms 2.0 fitted.dcd native.psf

The mrms flag tells carma to draw (in the rmsd plot) as black everything with an rms deviation larger that 2.0 Angstroem. The resulting postscript images (fitted.dcd.averag.ps and fitted.dcd.rmsdev.ps) can be view with, say, gv.

 average CA-CA and rms (graphs)

You can aid your analysis with

carma fitted.dcd.rmsdev.ps fitted.dcd.averag.ps gv carma.merged.ps

giving

 average CA-CA and rms merged