Functions
	rmsdOf sel1 sel2 ref1 ref2

	rmsfTrajectory sel ?win? ?step?

	rmsfTrajectoryColor sel ?win?

Detailed Description

Example

RMSD for all files (in a directory) and frames

Variables $compare and $reference should be two atomselections in different molecules. The former should be the TOP molecule.

 forFiles id {../filtered/ *.dcd} {
     set outch [open $id.rmsd w]
     forFrames fn $compare {
         set trans_mat [measure fit $compare $reference]
         $compare move $trans_mat
         set rmsd [measure rmsd $compare $reference]
         puts $outch "$rmsd $id $fn"
     }
     close $outch
 }

Function Documentation

◆ rmsdOf()

rmsdOf			sel1 sel2 ref1 ref2

Compute RMSD, over all frames, of a selection of atoms sel1 with respect to another sel2 after aligning the set of atoms ref1 to ref2. In ther words, for per each frame, align ref1 to ref2, and measure RMSD of sel1 with respect to sel2. sel1 and ref1 should belong to the same molecule (the trajectory under study, multiple frames). Sel2 and ref2 should belong to the same molecule (the reference frame). Return a list of RMSD values (one per frame in sel). If sel2 is the string ROTATE, RMSD is not computed, but sel1 is rotated instead.

◆ rmsfTrajectory()

rmsfTrajectory			sel ?win? ?step?

Compute average rmsf by sliding windows of width win. RMSF will be averaged by weight. See details in rmsfTrajectoryColor.

Parameters

sel	atom selection
win	window size (frames)
step	stride

◆ rmsfTrajectoryColor()

rmsfTrajectoryColor			sel ?win?

Compute average rmsf by sliding windows of width win. RMSF will be averaged by weight. Assign it to the "user" attribute at each frame, which will hold the RMSF computed over the next win frames.