VMD-L Mailing List
From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Mon Jul 18 2005 - 16:32:09 CDT
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Ken,
Maybe try moving the movesel into the loop, i.e.
# atom move and rmsd calculation loop
for {set i 1 } {$i < $nf } { incr i } {
set sel [atomselect $selid $seltext frame $i]
set movesel [atomselect $selid all frame $i]
$movesel move [measure fit $sel $ref]
puts $outfile "[measure rmsd $sel $ref]"
}
and remove it from outside the loop?
Chris
Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007
-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf Of Sale, Kenneth L
Sent: Monday, July 18, 2005 1:48 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l:
I am trying to overlay each frame of a trajectory onto another structure using the move command in a loop over the trajectory. However, the only frame that moves is the very last frame of the trajectory. My script is:
proc fit2mols_traj { refid reftext selid seltext } {
set ref [atomselect $refid $reftext]
set sel [atomselect $selid $seltext]
set movesel [atomselect $selid all]
set outfile [open rmsd.dat w];
set nf [molinfo $selid get numframes]
# atom move and rmsd calculation loop
for {set i 1 } {$i < $nf } { incr i } {
set sel [atomselect $selid $seltext frame $i]
$movesel move [measure fit $sel $ref]
puts $outfile "[measure rmsd $sel $ref]"
}
close $outfile
}
Is there some way to overlay each frame onto a common structure?
Thanks,
Ken
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