VMD-L Mailing List

From: Sara baretller (sarabiocomputation_at_gmail.com)
Date: Thu Jul 07 2011 - 08:08:42 CDT

Thank you so much for you help, i really appreciate your time and effort.

I am sorry but i am going to ask you what did you mean by set conv [expr
180/acos(-1.0)] # Using just the digits of pi that you remember is poor
practice
also what is the value "%5i" and "%7.2f " are they just examples...thank
you again

Sara

On Wed, Jul 6, 2011 at 1:34 PM, Mark Cunningham <cunningham_at_utpa.edu> wrote:

> Sara:
>
> If the values are not changing, it is undoubtably due to the fact that you
> are not
> incrementing the frame. If i is your frame index, you need a
> $sel1 frame $i
>
> As a cautionary note, atomselect is computationally expensive. It would be
> best
> to not recompute them. You can use the tcl array construct:
>
>
> for {set j 0} {$j < 6} {incr j} {
> set sel1($j) [atomselect $mol "residue $j and resname LEU and name
> BBc"]
> set sel2($j) [atomselect $mol "residue $j and resname GLU and name
> BBc"]
> }
>
> Inside your loop over the frames, you can access the stored selections:
> set vec2 {0 1 0} # This isn't changing so don't put
> it inside the loop
> set conv [expr 180/acos(-1.0)] # Using just the digits of pi that you
> remember is poor practice
> for {set i 0} {$i < $Nframes} {incr i} {
> puts -nonewline $outfile [format "%5i" $i]
>
> for {set j 0} {$j < 6}{incr j} {
> $sel1($j) frame $i
> $sel2($j) frame $i
> set coord1 [lindex [$sel1($j) get { x y z }] 0]
> set coord2 [lindex [$sel2($j) get { x y z }] 0]
> set vec1 [vecnorm[vecsub $coord1 $coord2 ]] #vecnorm will not fail
> if the vector length is 0 so
>
> #there's no particular reason to do the checking you do
> set angle [expr $conv*acos([vecdot $vec1 $vec2])]
> puts -nonewline [format "%7.2f " $angle] # this will write all 6
> angles on one line
> }
> puts $outfile " " # this will force a newline
> }
>
>
> Good luck
>
> Mark
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
> Sara baretller [sarabiocomputation_at_gmail.com]
> *Sent:* Wednesday, July 06, 2011 10:04 AM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: Re: Problem with for loop.
>
>
>
> Hi all
>
> please if you have an idea or suggestion , i would really appreciated it
>
> I solved the first problem , and the script worked and gave me the angle
> between the six peptides and the vector { 0 1 0} so i added another loop for
> the frames. for {set i 0} {$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
>>
>>
>