VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Aug 16 2018 - 11:22:21 CDT

With the logic you are proceeding in the script, is this correct???

        set zmax [expr $z0-10]

Still eyeballing your code. Perhaps you can tell us a bit more as in what
is happening and what do you expect to happen and someone can comment...

On Aug 16, 2018 23:56, "fan li" <fanliqmul_at_gmail.com> wrote:

> Hi everyone
>
> The suggestions from Ashar and Alex work fine for the part of code I posed
> in last email. But I can only get the right results for the first few
> frames and the results for other frames are not correct when I used their
> suggestions for my real script. The following is the real script I used.
>
> #########################################
> set zmin 30.3
>
> set nf [molinfo top get numframes]
> for {set i 0} {$i < $nf} {incr i} {
>
> #select sub2 and get the center
> set sub2($i) [atomselect top "resname sub2"]
> $sub2($i) frame $i
> $sub2($i) update
>
> #puts "$sub2 num\t"
>
> set cen_sub2 [measure center $sub2($i)]
>
> set x0 [lindex $cen_sub2 0]
>
> set y0 [lindex $cen_sub2 1]
>
> set z0 [lindex $cen_sub2 2]
>
> set xmin [expr $x0-10]
>
> set xmax [expr $x0+10]
>
> set ymin [expr $y0-10]
>
> set ymax [expr $y0+10]
>
> set zmax [expr $z0-10]
>
>
> puts "i=$i\t"
> puts "xmin=$xmin xmax=$xmax ymin=$ymin ymax=$ymax zmin=$zmin
> zmax=$zmax\t"
>
>
> #select water atoms within the region defined by the position
> condition
> set sel_water($i) [atomselect top "resname SOL and (x>$xmin and
> x<$xmax) and (y>$ymin and y<$ymax) and (z>$zmin and z<$zmax)"]
>
> $sel_water($i) frame $i
> $sel_water($i) update
>
> #reset the resname of the selected water
> $sel_water($i) set resname den
>
> puts "num of interested water=$sel_water($i)\t"
>
> set system($i) [atomselect top "all"]
> $system($i) frame $i
> $system($i) update
> $system($i) writegro "water_interest$i.gro"
>
> puts "num of all atoms=$system($i)\t"
>
> $sub2($i) delete
> $sel_water($i) delete
> $system($i) delete
>
>
> }
>
>
>
> #############################################################
>
> I have no idea what is going wrong? Could some one point the bug in the
> script?
>
> Fan
>
> Giacomo Fiorin <giacomo.fiorin_at_gmail.com> 于2018年8月16日周四 下午3:10写道：
>
>> Each VMD atom selection object contains internally vectors that are as
>> long as the total number of atoms in the molecule, and the memory usage of
>> these vectors will not change with the selection keyword. I think it'd be
>> safer to always delete an atom selection as soon as it's not needed.
>>
>> Giacomo
>>
>>
>> On Thu, Aug 16, 2018 at 10:00 AM João Ribeiro <jribeiro_at_ks.uiuc.edu>
>> wrote:
>>
>>> Also, if you need to create atom selections inside the loop (e.g. if
>>> zmin value changes), you should definitely delete the selection before the
>>> next iteration ("$sel_water($i) delete"), unless you need the atom
>>> selection for another operation outside the loop, or the selections don't
>>> take that much memory.
>>>
>>> Best
>>>
>>> João
>>>
>>> On Thu, Aug 16, 2018 at 8:14 AM Axel Kohlmeyer <akohlmey_at_gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Thu, Aug 16, 2018 at 7:17 AM fan li <fanliqmul_at_gmail.com> wrote:
>>>>
>>>>> Hi everyone
>>>>> I am trying to select atoms with specific region of SOL of each frame
>>>>> and change the selected atom's resname. I list part of my code below.
>>>>>
>>>>> ############################################
>>>>> set zmin 30.3
>>>>>
>>>>> set nf [molinfo top get numframes]
>>>>> for {set i 0} {$i < [expr (3-1)]} {incr i} {
>>>>>
>>>>> set sel_water($i) [atomselect top "resname SOL and z<$zmin"]
>>>>> $sel_water($i) frame $i
>>>>>
>>>>> #reset the resname of the selected water
>>>>> $sel_water($i) set resname den
>>>>>
>>>>> $sel_water($i) writegro "water_interest$i.gro"
>>>>>
>>>>> }
>>>>>
>>>>>
>>>>>
>>>>> ########################################
>>>>> This "set sel_water($i) [atomselect top "resname SOL and z<$zmin"]"
>>>>> selection is not working properly as the outcome is not the region I
>>>>> specified.
>>>>>
>>>>> Then I removed the "z<$zmin" and changed it to "set sel_water($i)
>>>>> [atomselect top "resname SOL"]", it woks fine as the entire water is
>>>>> selected.
>>>>>
>>>>> So could someone tell me why the selection is not working with the
>>>>> position selected condition is not working?
>>>>>
>>>>> As position selected condition changes over each frame in the actual
>>>>> code, so I can not put the selection outside the loop?
>>>>>
>>>>
>>>> that last statement is not correct something like this:
>>>>
>>>> $sel frame $i
>>>> $sel update
>>>>
>>>> will re-evaluate the selection stored in $sel for the frame $i (that
>>>> is, for as long as $zmin doesn't change, as the selection string will
>>>> evaluate variables when the selection is defined and not re-evaluate it
>>>> when updated).
>>>>
>>>> axel.
>>>>
>>>>
>>>>
>>>>>
>>>>> Fan
>>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>
>>>
>>>
>>> --
>>> ……………………………………………………...
>>> João Vieira Ribeiro
>>> Theoretical and Computational Biophysics Group
>>> Beckman Institute, University of Illinois
>>> http://www.ks.uiuc.edu/~jribeiro/
>>> jribeiro_at_ks.uiuc.edu
>>> +1 (217) 3005851
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>