VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jul 06 2011 - 10:57:44 CDT

nobody can help you to debug script code without seeing the script.
i've been trying to do psychic debugging for years and it almost
always failed miserably.

axel.

On Wed, Jul 6, 2011 at 11:04 AM, Sara baretller
<sarabiocomputation_at_gmail.com> wrote:
>
>
> 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
>>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.