From: kim, stephanie S. (
Date: Wed Aug 03 2016 - 11:31:37 CDT


I've tried to align a trajectory of a protein consisting two chains, but when I load the aligned version of the trajectory, two chains separate, jump around for couple of frames and then would come back. A colleague suggested using ptraj commands: "center" and "image center familiar" instead, because he had the same problem before with aligning a trajectory consisting two subunits using vmd.

Can you suggest any other tcl scripts that would fix this problem? Or could you suggest a script that correlates to the ptraj command "center" and "image center familiar"?

I've used this script to align the trajectory:


proc align { rmolid smolid2 seltext } {
  set ref [atomselect $rmolid $seltext frame 0]
  set sel [atomselect $smolid2 $seltext]
  set all [atomselect $smolid2 all]
  set n [molinfo $smolid2 get numframes]

  for { set i 1 } { $i < $n } { incr i } {
    $sel frame $i
    $all frame $i
    $all move [measure fit $sel $ref]
$ref delete
$all delete
$sel delete

align 0 0 "protein"


Thank you,

Stephanie Kim

Graduate Student

Department of Chemistry and Biochemistry

The Ohio State University

2116 Newman & Wolfrom Laboratory

100 W. 18th Ave
Columbus, OH 43210