VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 11 2011 - 11:49:39 CST
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- In reply to: Ajasja Ljubetič: "Re: tcl script"
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On Fri, Mar 11, 2011 at 11:17 AM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com> wrote:
> Hi,
> you have to move the set A and set B calls inside the loop
...and delete the $sel# update calls.
the selection will not change and the update is time consuming.
without, the script will give the same result faster.
cheers,
axel.
> set mol [molinfo top]
> set sel1 [atomselect $mol "resname UNK"]
> set sel2 [atomselect $mol "resid 200"]
> set frames [molinfo $mol get numframes]
> for {set i 0} {$i < $frames} {incr i} {
> $sel1 frame $i
> $sel2 frame $i
> $sel1 update
> $sel2 update
> set A [lindex [$sel1 get { x y z }] 0]
> set B [lindex [$sel2 get { x y z }] 0]
> set distAB [vecdist $A $B]
> puts "$i $distAB"
> }
> regards,
> Ajasja
> On Fri, Mar 11, 2011 at 16:06, ban arn <ban.arn_at_gmail.com> wrote:
>>
>> Dear VMD users
>>
>> I'm new to tcl scripting and i'm thankful to help or suggestion.
>>
>> In tcl script for calculating the distance between center of mass of
>> ligand and residues along the trajectory, I'm trying to loop over the
>> trajectory, but I couldn't able to update the frames along the time.
>>
>> Kindly find the script here:
>>
>> set mol [molinfo top]
>> set sel1 [atomselect $mol "resname UNK"]
>> set sel2 [atomselect $mol "resid 200"]
>> set A [lindex [$sel1 get { x y z }] 0]
>> set B [lindex [$sel2 get { x y z }] 0]
>> set distAB [vecdist $A $B]
>> set frames [molinfo $mol get numframes]
>> for {set i 0} {$i < $frames} {incr i} {
>> $sel1 frame $i
>> $sel2 frame $i
>> $sel1 update
>> $sel2 update
>> set n [vecdist $A $B]
>> puts "$i $n"
>> }
>>
>> Kindly advice
>>
>> Many Thanks
>> Balaji
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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