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From: Sara baretller (sarabiocomputation_at_gmail.com)
Date: Fri Jul 01 2011 - 13:13:14 CDT
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I will really appreciate any help or suggestion.
the script is for getting a vector of two selections of a peptide and then
the angle of this vector with another vector.
the script it will calculate the vectors and the angle for the first loop
fine however when i run the script in the tcl council it gives me the
vectors and angle for the first loop(residue 0 of 6 ) but then it will not
go for the next (residue 1 of 6) , 2,3,4,5, and so far till the 6th (
peptide 6)
the Tcl counsel gives me this:
residue 0 of 6 peptides
atomselect28 atomselect29
1 1
{39.70000076293945 -4.400000095367432 53.599998474121094} {46.10000228881836
4.899999618530273 37.099998474121094}
-6.400001525878906 -9.299999713897705 16.5
vec1l vec2l : 19.99249894859944 1.0
dotprod: -0.46517445056808215
angle 2.0546279983239657
Final angle : 117.72161220856759
117.72161220856759
*I dont know why it s not going to next peptide , please if you can help.
it was going to the next peptide before i added the part of the vector and
the angle. i can not figure out whats the problem is now.*
script is:
set outfile [open "out_vecot.dat" "w"]
for {set j 0} {$j < 6} {incr j} {
set mol [molinfo top]
set sel1 [atomselect $mol "residue $j and resname LEU and
name BBc"]
set sel2 [atomselect $mol "residue $j and resname GLU and
name BBc"]
$sel1 frame $j
$sel2 frame $j
$sel1 update
$sel2 update
puts "residue $j of 6 peptides"
puts "$sel1 $sel2"
set nLEU [llength [$sel1 list]]
set nGLU [llength [$sel2 list]]
puts " $nLEU $nGLU"
set coord1 [$sel1 get { x y z }]
set coord2 [$sel2 get { x y z }]
puts "$coord1 $coord2"
set vec1 [vecsub [lindex $coord1 0] [lindex $coord2 0]]
puts "$vec1"
set vec2 {0 1 0}
set vec1l [veclength $vec1]
set vec2l [veclength $vec2]
puts " vec1l vec2l : $vec1l $vec2l"
if {$vec1l != 0} {
set vec1 [vecnorm $vec1]
}
if {$vec2l != 0} {
set vec2 [vecnorm $vec2]
}
set dotprod [vecdot $vec1 $vec2]
puts " dotprod: $dotprod"
set angle [expr acos($dotprod)]
puts "angle $angle"
set angle [expr ($angle * 180/3.14159)]
puts "Final angle : $angle"
return $angle
puts $outfile "$j $angle"
}
close $outfile
Thank you
Sara
- Next message: Sara baretller: "Re: Problem with loop. it s not going to the next peptide"
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- Next in thread: Sara baretller: "Re: Problem with loop. it s not going to the next peptide"
- Reply: Sara baretller: "Re: Problem with loop. it s not going to the next peptide"
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