VMD-L Mailing List

From: Viviane Corrêa (vivicorreasantos_at_gmail.com)
Date: Fri Feb 07 2020 - 07:31:56 CST

Hello all, you're right. I used "resid 216" and it worked.

Thanks a lot!

Viviane

Em sex., 7 de fev. de 2020 às 13:17, Giacomo Fiorin <
giacomo.fiorin_at_gmail.com> escreveu:

> Hello Viviane, "216" is not a valid atom selection string. Number 216 may
> have been for example an atom by *index* (0-based), by *serial* number
> (1-based), the *resid* number (which can occur multiple times in
> different chains), the *residue* number (unique in the whole system), or
> the *fragment* number, etc.
>
> Check the doc for the atomselect command to find out how to express for
> VMD the selection you have in mind.
>
> Giacomo
>
> On Fri, Feb 7, 2020 at 5:07 AM Viviane Corrêa <vivicorreasantos_at_gmail.com>
> wrote:
>
>> 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>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
> 

-- 
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>