VMD-L Mailing List
From: kim, stephanie S. (kim.6088_at_buckeyemail.osu.edu)
Date: Wed Aug 03 2016 - 11:31:37 CDT
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Hello,
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
return
}
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
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