VMD-L Mailing List

From: Sunita Patel (sunita.patel_at_cbs.ac.in)
Date: Thu Feb 18 2021 - 23:07:53 CST

Dear Users,

I made the suggested changes and deleted the variables after their use. Now
the script is showing improved performance.
Thank you so much!

Sincerely,
Sunita

On Thu, Feb 18, 2021 at 1:23 PM Norman Geist <norman.geist_at_uni-greifswald.de>
wrote:

> As Axel pointed out, you have to delete the atomselect objects.
>
>
>
> Example:
>
>
>
> for {set f 0} {$f <= $frames} {incr f} {
>
> set a [atomselect top “protein”]; #<-- this is the memory
> leak
>
>
>
> #do something with a
>
>
>
> #by the end of the loop, once you no longer need a, delete
> it
>
> $a delete
>
> }
>
>
>
> Bests
>
> Norman Geist
>
>
>
>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Sunita Patel
> *Gesendet:* Donnerstag, 18. Februar 2021 07:36
> *An:* vmd-l_at_ks.uiuc.edu
> *Betreff:* Re: vmd-l: Native contacts tcl script crashed
>
>
>
> Dear VMD-users,
>
>
>
> I have rewritten the vmd script considering your suggestions. After each
> frame comparison I am deleting the list variable (unset var) and
> re-assigning new values to the same variable for comparison with the next
> frame. It is working fine up to 80 frames. For hundreds of frames it is
> again crashing in GUI mode. I tried running it in vmdtext mode which is
> working fine but it is very slow.
>
>
>
> Could anybody see my code and recommend where I need to improve. The tcl
> script is attached and also appended in this email. Should I send test
> input files?
>
>
>
> Thank you so much for your help.
>
>
>
> Sincerely,
>
> Sunita
>
>
>
> ==========
>
> # Usage "source vmd_native_contacts.tcl" source vmd_native_contact 0.
> # First frame is considered as reference native structure.
> proc vmd_native_contacts { mol } {
> puts "Enter output file name:"
> set outputfilename [gets stdin]
> set output [open $outputfilename w]
> set allCa [atomselect $mol "name CA"]
> #get the index of CA atoms
> set rid [$allCa get index]
> # No. of C-alphas
> set ridLength [llength $rid]
> set num [molinfo $mol get numframes]
> set k 0 ;
> # Iteration over frames
> while {$k < $num} {
> set allpairs {};
> set NC 0;
> #compare the CA atoms pair which are separated by 6.5 Ang or less
> for {set i 0} {$i < $ridLength} {incr i} {
> for {set j [expr $i+4]} {$j < $ridLength} {incr j} {
> set fir [lindex $rid $i];
> set sec [lindex $rid $j];
> set firNdx [atomselect $mol "index $fir" frame $k];
> set secNdx [atomselect $mol "index $sec" frame $k];
> set firCen [measure center $firNdx];
> set secCen [measure center $secNdx];
> set diff [vecsub $firCen $secCen];
> set dist [veclength $diff];
> if {$dist < 6.5} {
> if {$k == 0} {
> lappend refContacts "$fir $sec" ; }
> if {$k != 0} {
> lappend allpairs "$fir $sec" ; }
> }
> }
> }
> set LrefNC [llength $refContacts]
> for {set n 0} {$n < $LrefNC} {incr n} {
> set refNC [lindex $refContacts $n];
> set search [lsearch $allpairs "$refNC"]
> if {$search != -1} {
> set NC [expr $NC + 1]
> }
> }
> unset allpairs;
> # It gives frame versus number of native contacts.
> set pcgNC [expr ([format %8.1f $NC] / [format %8.1f $LrefNC]) * 100]
> puts $output "$k [format %8.1f $pcgNC]" ;
> flush $output;
> set k [expr $k + 1]
> }
> }
>
> ================================
>
>
>
> On Tue, Feb 16, 2021 at 4:57 PM Ashar Malik <asharjm_at_gmail.com> wrote:
>
> Haven't had a detailed look through your code.
>
>
>
> Just a quick point though, that if you make a selection, do delete it when
> you are done with using it.
>
>
>
> This should be a fix if memory is the only issue with your code.
>
>
>
>
>
>
>
> On Tue, Feb 16, 2021 at 7:05 PM Sunita Patel <sunita.patel_at_cbs.ac.in>
> wrote:
>
> Dear VMD-users,
>
>
>
> I wrote a tcl script to find the number of native contacts in each frame.
> The reference frame (frame 0) whose native contacts have been matched with
> other frames. This program is working fine with a small number of frames
> (frames 30). However it crashed when I ran the program for 400 frames.
>
>
>
> I need your help to rectify the program so that it will work for a larger
> number of frames. Please find the program appended below or also as an
> attachment.
>
>
>
> Your help will be highly appreciated.
>
>
>
> Sincerely,
>
> Sunita
>
> ============================================================
>
> # Usage "source vmd_native_contacts.tcl" source vmd_native_contact 0.
> # First frame is considered as reference native structure.
> proc vmd_native_contacts { mol } {
> puts "Enter output file name:"
> set outputfilename [gets stdin]
> set output [open $outputfilename w]
>
> set allCa [atomselect $mol "name CA"]
> #get the index of CA atoms
> set rid [$allCa get index]
> # No. of C-alphas
> set ridLength [llength $rid]
> set num [molinfo $mol get numframes]
> set k 0 ;
> set allcontacts {}
> # Iteration over frames
> while {$k < $num} {
> set ctr 0
> set contactCa {}
> #compare the CA atoms pair which are separated by 6.5 Ang or less
> for {set i 0} {$i < $ridLength} {incr i} {
> for {set j [expr $i+4]} {$j < $ridLength} {incr j} {
> set fir [lindex $rid $i];
> set sec [lindex $rid $j];
> set firNdx [atomselect $mol "index $fir" frame $k];
> set secNdx [atomselect $mol "index $sec" frame $k];
> set firCen [measure center $firNdx];
> set secCen [measure center $secNdx];
> set diff [vecsub $firCen $secCen];
> set dist [veclength $diff];
> if {$dist < 6.5} {
> set ctr [expr $ctr + 1]
> lappend contactCa "$fir $sec" ;
> }
> }
> }
> # CA-atomd distance less than 6.5 are put in the list 'allcontacts'.
> lappend allcontacts "$contactCa" ;
> set k [expr $k + 1]
> }
>
> # No. of native contacts in the reference structure that is 'frame 0'.
> set nrefNc [llength [lindex $allcontacts 0]];
> # No. of frames 'fr'.
> set fr [llength [lindex $allcontacts]];
> # Searching of native contacts from frame 1 onwards (frame 0 is the
> reference)
> for {set m 1} {$m < $fr} {incr m} {
> set Ncontact 0
> for {set n 0} {$n < $nrefNc} {incr n} {
> set refNc [lindex $allcontacts 0 $n];
> set search [lsearch [lindex $allcontacts $m] "$refNc"]
> if {$search != -1} {
> set Ncontact [expr $Ncontact + 1]
> }
> }
> set pcgNC [expr ([format %8.1f $Ncontact] / [format %8.1f $nrefNc]) * 100]
> puts $output "$m [format %8.1f $pcgNC]";
> flush $output;
> }
> }
>
> ====================================================
>
>
>
>