MBG wiki: Calculation of the average structure and corresponding fluctuations

xplor saves the day :

structure @native.psf end

dynamics analysis average

  asci=false
  input=fitted.dcd
  begin=0 skip=1 stop=2000000

  reference=aver

end

write coordinates output=aver_and_rms.pdb end

stop

The DCD file that you feed to xplor must have global rotations-translations removed.

Edit aver_and_rms.pdb and remove the header lines. Save the modified file. The B-factor column contains rms fluctuations for the corresponding atoms. View it :

rasmol aver_and_rms.pdb
restrict not hydrogen
cpk
color temperature
wireframe off
cpk off
cartoon

Use your editor to select the B-value column (ie the fluctuations) of the Cα atoms only and save them to file. Use xmgr to make a graph of how the rms fluctuations change across the structure.