MBG wiki | RecentChanges | Blog | 2025-09-20 | 2025-09-19

gyration.tcl

proc gyration {{mol top}} {
	#use frame 0 for reference
	#set reference [atomselect $mol "name CA" frame 0]
	#the frame being compared
	set compare [atomselect $mol "name CA"]
	
	set num_steps [molinfo $mol get numframes]


	set file [open gyr-t w]

	for {set frame 0} {$frame < $num_steps} {incr frame} {
		#get the correct frame
		$compare frame $frame
		
		#compute the transformation
		set gyr [measure rgyr $compare]
		#do the alignment
		#$compare move $trans_mat
		#compute the rmsd
		#set rmsd [measure rmsd $compare $reference]
		#print the rmsd
		#puts "$frame $gyr"
		
    		puts $file "$frame $gyr"

	}

	close $file
	
}

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