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From: Murpholino Peligro (murpholinox_at_gmail.com)
Date: Thu Mar 08 2012 - 15:33:19 CST
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Hi all!
I want to know the average distance for alpha carbons in my protein with N
residues (in this case 111)
I was trying to get the distance for residue i and that of residue i-1
Until now I have>
set file [open "ca-dist.dat" w]
for { set i 2 } { $i <= 111 } { incr i } {
set j 0
for { set j [ expr $i - 1 ] } { $j <= [ expr $i -1 ] } { incr j } {
set seli [[atomselect top "protein and name CA and resid $i"] get
index]
set selj [[atomselect top "protein and name CA and resid $j"] get
index]
puts "$j $selj $i $seli" ;# everything is ok 'til here
set dist 0 ;# not sure if this line is correct
set dist [ measure bond {"$selj $seli"} ] ;# I think the problem
are the double quotes, but I really don't have idea
puts "$j $i $dist"
}; # for j
}; # for i
close $file
Any help with the code is appreciated
loading the ca-dist.dat into R in this way I can get the average distance
very easy and do some plots
Ps ca-dist.tcl is somewhat different of what I want
-- Mr. Murpholino X "mi segundo nombre es Peligro!!"
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