VMD-L Mailing List

From: Sara baretller (sarabiocomputation_at_gmail.com)
Date: Wed Jul 06 2011 - 10:04:01 CDT

Hi all

please if you have an idea or suggestion , i would really appreciated it

I solved the first problem , and the script worked and gave me the angle
between the six peptides and the vector { 0 1 0} so i added another loop for
the frames. for {set i 0} {$i < 8} {incr i} { , 8 as an example.

 it gave me the same results over and over again for the frames.

here the loop is only till frame 8 as an example:

the repeat for all the angle but i highlighted two anglesas an example that
keep repeating between from the first frame to the other frame. angle
117.72161220856759 between (peptides 0)'s vector and the vector { 0 1 0} in
frame 0. is the same as angle 117.72161220856759 between peptides 1 vector
and the vector { 0 1 0} in frame 1 and so on.

 i alos hilighted : 55.63259488419982 for the height frame

Tcl Counsel results:

residue 0 of 6 peptides
 vec1l vec2l : 19.99249894859944 1.0
Final angle : 117.72161220856759
117.72161220856759
0
residue 1 of 6 peptides
 vec1l vec2l : 18.69491870304378 1.0
Final angle : 135.78875014576658
135.78875014576658
0
residue 2 of 6 peptides
 vec1l vec2l : 27.989461118438296 1.0
Final angle : 55.63259488419982
55.63259488419982
0
residue 3 of 6 peptides
 vec1l vec2l : 27.10166056426399 1.0
Final angle : 93.17285877063786
93.17285877063786
0
residue 4 of 6 peptides
 vec1l vec2l : 29.5839470751503 1.0
Final angle : 145.5654673648764
145.5654673648764
0
residue 5 of 6 peptides
 vec1l vec2l : 25.998842961169046 1.0
Final angle : 87.57519131337723
87.57519131337723
0
residue 0 of 6 peptides
 vec1l vec2l : 19.99249894859944 1.0
Final angle : 117.72161220856759
117.72161220856759
1
residue 1 of 6 peptides
 vec1l vec2l : 18.69491870304378 1.0
Final angle : 135.78875014576658
135.78875014576658
1
residue 2 of 6 peptides
 vec1l vec2l : 27.989461118438296 1.0
Final angle : 55.63259488419982
55.63259488419982
1
residue 3 of 6 peptides
 vec1l vec2l : 27.10166056426399 1.0
Final angle : 93.17285877063786
93.17285877063786
1
residue 4 of 6 peptides
 vec1l vec2l : 29.5839470751503 1.0
Final angle : 145.5654673648764
145.5654673648764
1
residue 5 of 6 peptides
 vec1l vec2l : 25.998842961169046 1.0
Final angle : 87.57519131337723
87.57519131337723
1
residue 0 of 6 peptides
 vec1l vec2l : 19.99249894859944 1.0
Final angle : 117.72161220856759
117.72161220856759
2
residue 1 of 6 peptides
 vec1l vec2l : 18.69491870304378 1.0
Final angle : 135.78875014576658
135.78875014576658
2
residue 2 of 6 peptides
 vec1l vec2l : 27.989461118438296 1.0
Final angle : 55.63259488419982
55.63259488419982
2
residue 3 of 6 peptides
 vec1l vec2l : 27.10166056426399 1.0
Final angle : 93.17285877063786
93.17285877063786
2
residue 4 of 6 peptides
 vec1l vec2l : 29.5839470751503 1.0
Final angle : 145.5654673648764
145.5654673648764
2
residue 5 of 6 peptides
 vec1l vec2l : 25.998842961169046 1.0
Final angle : 87.57519131337723
87.57519131337723
2
residue 0 of 6 peptides
 vec1l vec2l : 19.99249894859944 1.0
Final angle : 117.72161220856759
117.72161220856759
3
residue 1 of 6 peptides
 vec1l vec2l : 18.69491870304378 1.0
Final angle : 135.78875014576658
135.78875014576658
3
residue 2 of 6 peptides
 vec1l vec2l : 27.989461118438296 1.0
Final angle : 55.63259488419982
55.63259488419982
3
residue 3 of 6 peptides
 vec1l vec2l : 27.10166056426399 1.0
Final angle : 93.17285877063786
93.17285877063786
3
residue 4 of 6 peptides
 vec1l vec2l : 29.5839470751503 1.0
Final angle : 145.5654673648764
145.5654673648764
3
residue 5 of 6 peptides
 vec1l vec2l : 25.998842961169046 1.0
Final angle : 87.57519131337723
87.57519131337723
3
residue 0 of 6 peptides
 vec1l vec2l : 19.99249894859944 1.0
Final angle : 117.72161220856759
117.72161220856759
4
residue 1 of 6 peptides
 vec1l vec2l : 18.69491870304378 1.0
Final angle : 135.78875014576658
135.78875014576658
4
residue 2 of 6 peptides
 vec1l vec2l : 27.989461118438296 1.0
Final angle : 55.63259488419982
55.63259488419982
4
residue 3 of 6 peptides
 vec1l vec2l : 27.10166056426399 1.0
Final angle : 93.17285877063786
93.17285877063786
4
residue 4 of 6 peptides
 vec1l vec2l : 29.5839470751503 1.0
Final angle : 145.5654673648764
145.5654673648764
4
residue 5 of 6 peptides
 vec1l vec2l : 25.998842961169046 1.0
Final angle : 87.57519131337723
87.57519131337723
4

On Wed, Jul 6, 2011 at 10:38 AM, Sara baretller <
sarabiocomputation_at_gmail.com> wrote:

>
> I have been having a problem with this script , I will really appreciate
> your help. so the script does get me the angle between two vectors but then
> it will not go to the next loop. it stops in the first. by giving the angle
> between the first vector and the vector {0 1 0 }.
>
>
>
> Script:
>
> for {set j 0} {$j < 6} {incr j} {
>
> set outfile [open "out.dat" "w"]
>
> 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 [$sel2 list]]
>
> set coord1 [$sel1 get { x y z }]
> set coord2 [$sel2 get { x y z }]
>
>
> set vec1 [vecsub [lindex $coord1 0] [lindex $coord2 0]]
>
> set vec2 {0 1 0}
>
> set vec1l [veclength $vec1]
> set vec2l [veclength $vec2]
>
> if {$vec1l != 0} {
> set vec1 [vecnorm $vec1]
> }
> if {$vec2l != 0} {
> set vec2 [vecnorm $vec2]
> }
>
> set dotprod [vecdot $vec1 $vec2]
>
> set angle [expr acos($dotprod)]
>
> set angle [expr ($angle * 180/3.14159)]
> puts "Final angle : $angle"
> puts $angle
> }
>
> close $outfile
>
> tcl councel:
>
> angle 1.5284741404344042
> Final angle : 87.57519131337723
> 87.57519131337723
>
>
> Thank you
>
> Sara
>
>