VMD-L Mailing List

From: Viviane Corrêa (vivicorreasantos_at_gmail.com)
Date: Fri Feb 07 2020 - 03:37:47 CST

Hello John Stone,

I loaded the trajectory and from the VMD TkConsole I sourced the script.

Then I typed: contactFreq "protein" "216"

and I got this message: atomselect: cannot parse selection text: protein
and noh and within 4 of (216 and noh)

I found the script here:
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19311.html

Thanks for your help!

Viviane

Em qui., 6 de fev. de 2020 às 18:40, John Stone <johns_at_ks.uiuc.edu>
escreveu:

> Hi,
> Okay, now we have the script, but you haven't actually asked a
> well-formed question. Please provide as much other information that you
> can so that someone could use it to help you.
>
> I assume you're having some trouble and that you're getting an
> atom selection error. You haven't told us what steps you have done,
> where the script came from, what kind of machine you're
> running on, and so on.
>
> At the very minimum we need to see what command(s) you ran.
> You can see that the script uses the parameters "sel1" and "sel2"
> to create its atom selections. If you provide invalid inputs for
> sel1 or sel2, you will definitely get an error when using that script.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Feb 06, 2020 at 06:31:06PM +0100, Viviane Corrêa wrote:
> > Now the attachment...
> > Em qui., 6 de fev. de 2020 Ã s 18:21, John Stone <[1]
> johns_at_ks.uiuc.edu>
> > escreveu:
> >
> > Hi,
> > Â There was no attachment on your posting.
> > If the attachment is too big, the mailing list software will remove
> it
> > to prevent it from creating trouble for recipients with small
> > mailbox storage limits.
> >
> > Best regards,
> > Â John Stone
> > Â [2]vmd_at_ks.uiuc.edu
> >
> > On Thu, Feb 06, 2020 at 06:13:25PM +0100, Viviane CorrÄ*a wrote:
> > > Hi,
> > >
> > > I'm trying to analyze the frequency of contacts between the
> protein
> > and a
> > > small molecule (residue 216). I'm using the attached script
> > contactFreq.tcl
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > [3]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone:
> 217-244-3349
> > [4]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
> >
> > --
> > Viviane Corrêa Santos, MSc
> > Protein Computational Biology Group
> > Departamento de BioquÃmica e Imunologia - ICB - UFMG
> > [5]www.biocomp.icb.ufmg.br
> >
> > References
> >
> > Visible links
> > 1. mailto:johns_at_ks.uiuc.edu
> > 2. mailto:vmd_at_ks.uiuc.edu
> > 3. http://www.ks.uiuc.edu/~johns/
> > 4. http://www.ks.uiuc.edu/Research/vmd/
> > 5. http://www.biocomp.icb.ufmg.br/biocomp/?page_id=232
>
> > proc contactFreq { {sel1} {sel2} {percent 0} {outFile stdout} {mol top}
> } {
> > if { $outFile != "stdout" } {
> > set outFile [open $outFile w]
> > }
> > puts $outFile "[clock format [clock scan now]] Search started."
> >
> > set allAtoms {}
> > set allCount {}
> > set numberOfFrames [molinfo $mol get numframes]
> > for { set i 0 } { $i < $numberOfFrames } { incr i } {
> > molinfo $mol set frame $i
> >
> > set frameCount {}
> > set frameAtoms [atomselect $mol "$sel1 and noh and within 4 of
> ($sel2 and noh)"]
> > foreach {segid} [$frameAtoms get segid] {resname} [$frameAtoms get
> resname] {resid} [$frameAtoms get resid] {name} [$frameAtoms get name] {
> > set atom [list $resid $resname $segid]
> > if {[lsearch $frameCount $atom] != -1} continue
> > lappend frameCount $atom
> > set loc [lsearch $allAtoms $atom]
> > if { $loc == -1 } {
> > lappend allAtoms $atom
> > lappend allCount 1
> > } else {
> > lset allCount $loc [expr { [lindex $allCount $loc] + 1 } ]
> > }
> > }
> > $frameAtoms delete
> > }
> >
> > puts $outFile "[clock format [clock scan now]] Search finished."
> >
> > puts $outFile "Find interactions:"
> > puts $outFile "Residue \t\tfraction"
> > #print count after sorting
> > set outData {}
> > foreach { a } $allAtoms { c } $allCount {
> > lappend outData [concat $c $a]
> > }
> > foreach { data } [lsort -integer -index 1 $outData] {
> > set c [lindex $data 0]
> > set fraction [expr { 100*$c/($numberOfFrames+0.0) }]
> > if { $fraction >= $percent } {
> > puts $outFile [format "%s-%s-%s \t\t %.2f%%" [lindex $data 3]
> [lindex $data 2] [lindex $data 1] $fraction]
> > }
> > #set beta according to the fraction, this is optional
> > set atom [atomselect $mol "segid [lindex $data 3] and resname
> [lindex $data 2] and resid [lindex $data 1]"]
> > $atom set beta $fraction
> > $atom delete
> > }
> >
> > if { $outFile != "stdout" } {
> > close $outFile
> > }
> >
> > }
> >
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
Viviane Corrêa Santos, MSc
Protein Computational Biology Group
Departamento de Bioquímica e Imunologia - ICB - UFMG
www.biocomp.icb.ufmg.br
<http://www.biocomp.icb.ufmg.br/biocomp/?page_id=232>
<http://www.biocomp.icb.ufmg.br/biocomp/?page_id=252>