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From: PARMINDER MANKOO (pmankoo1_at_jhu.edu)
Date: Tue Jun 26 2007 - 15:46:02 CDT
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Hello,
I am trying to write a script to compute the angle bween two domains in my protein for a time trajectory. The two domains have resid (591 to 746) and (747 to 961).
One way is to compute the center of coordinate for these two domains and use a residue in the middle of two domains as the third point. Following script is what I have written. Is this okay? And how can I do it over time trajectory (the dcd files, I am reading from CHARMM?).
Thanks, preeti
set DC [atomselect top "resid 591 to 746"]
set AC [atomselect top "resid 747 to 961"]
set HC [atomselect top "resid 747"]
> >
puts $cen1 "DC center [measure center $DC]"
puts $cen2 "AC center [measure center $AC]"
puts $cen3 "HC center [measure center $HC]"
> >
> >
proc angle {DC HC AC} {
# cosine of the angle between three points
# cos = ( v1 * v2 ) / |v1| * |v2|, where v1 and v2 are vectors
# get Pi 3.14159265358979323846
global M_PI
> >
# setup vectors hd and ha
set hd [vecsub $DC $HC]
set ha [vecsub $AC $HC]
set cosine [expr [vecdot $hd $ha] / ( [veclength $hd] * [veclength $ha])]
> >
# convert cosine to angle in degrees
return [expr acos($cosine)*(180.0/$M_PI)]
> >
}
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