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From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Wed Feb 13 2008 - 10:18:19 CST
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Hi,
I get different results when I use the RMSD Trajectory tool and my script
below - both of them should align to a reference structure and then compute
the RMSD. The problem is that I get different numbers depending on which
method I use - I would expect them to be identical..
VMD Script
0.310802847147 0.334529817104
Any help or comments appreciated
Thanks in advance
Best
J
proc print_rmsd_through_time {{mol top}} {
# use frame 0 for the reference
set reference [atomselect $mol "protein" frame 0]
# the frame being compared
set compare [atomselect $mol "protein"]
set num_steps [molinfo $mol get numframes]
for {set frame 0} {$frame < $num_steps} {incr frame} {
# get the correct frame
$compare frame $frame
# compute the transformation
set trans_mat [measure fit $compare $reference]
# do the alignment
$compare move $trans_mat
# compute the RMSD
set rmsd [measure rmsd $compare $reference]
# print the RMSD
puts "RMSD of $frame is $rmsd"
}
}
print_rmsd_through_time
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