VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Nov 03 2017 - 18:16:55 CDT

Yes, the puts $file is in the wrong place. I haven't read the details of
your code, but this is the necessary change

puts "$i $j [veclength [vecsub [measure center [lindex $ressellist $i]]
[measure center [lindex $ressellist $j]]]]"

should become

puts $fp "$i $j [veclength [vecsub [measure center [lindex $ressellist $i]]
[measure center [lindex $ressellist $j]]]]"

In general, if it is showing up on the Tk console window, it isn't being
written to the file. So if it works correctly, you should just see a frozen
Tk console screen until the script finishes running.

HTH.
Chitrak.

On Fri, Nov 3, 2017 at 5:29 PM, Windle,Stephen <snw42_at_drexel.edu> wrote:

> Thank you all for your tips. They've been most helpful. If I've learned
> anything in coding, it's that fixing one problem leads to another. This is
> no exception. For some reason, my output file is empty. The numbers I want
> are showing up in the TK Console just not making it to the file. I am
> assuming I'm doing something foolish with the script. Here it is (it's a
> slightly adjusted variation of what was already posted on this thread):
>
>
> set allsel [atomselect top "sidechain and resname ALA"]
> set residuelist [lsort -unique -integer [$allsel get residue]]
>
> set ressellist [list ]
> foreach residue $residuelist {
> lappend ressellist [atomselect top "residue $residue"]
> }
>
> set file [open "myoutput.dat" w]
>
> puts $file [
> for { set i 0 } { $i < [llength $ressellist] } { incr i } {
> for { set j [expr {$i+1}] } { $j < [llength $ressellist] } { incr j } {
> puts "$i $j [veclength [vecsub [measure center [lindex $ressellist $i]]
> [measure center [lindex $ressellist $j]]]]"
> }
> }
> ]
>
> close $file
>
> Am I putting my "puts $file" command in the wrong place? Should it go
> inside the for loop? Thanks again!
>
>
> -Steve
> ------------------------------
> *From:* Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> *Sent:* Tuesday, October 31, 2017 7:03:12 PM
> *To:* Windle,Stephen; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Computing atom distances
>
> Hi Steve,
>
> Tcl can be a messy beast. :) In terms of loading every single pdb in a
> directory, that is fairly simple:
>
> set pdblist [glob *.pdb]
> foreach pdb $pdblist {
> mol new $pdb
> }
>
> Now you want to make some sort of measurement afterward. This also isn't
> *too* bad, but it really depends on what exactly you want to be measuring,
> why, and what kind of data format you want to get out. The simplest way
> might be something like this:
>
> set allsel [atomselect top "protein"]
> set residuelist [lsort -unique -integer [$allsel get residue]]
>
> set ressellist [list ]
> foreach residue $residuelist {
> lappend ressellist [atomselect top "residue $residue"]
> }
>
> for { set i 0 } { $i < [llength $ressellist] } { incr i } {
> for { set j [expr {$i+1}] } { $j < [llength $ressellist] } { incr j } {
> puts "$i $j [veclength [vecsub [measure center [lindex $ressellist $i]]
> [measure center [lindex $ressellist $j]]]]"
> }
> }
>
> This will measure the distance between any pair of protein residues in the
> top molecule, while only making a relatively small number of
> atomselections. Things a beginning VMDer should definitely read are the
> userguide (https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fcurrent%
> 2Fug&data=02%7C01%7Csnw42%40drexel.edu%7C5c2434391fd84f23ac4008d520b394ae%
> 7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C636450878022113423&sdata=
> gxGdXXLbFoeDc9lfFAvLPVhuXoDGk5c%2B%2BZjsY%2BZJ6Is%3D&reserved=0),
> particularly the sections about Tcl/Tk scripting, and the available vector
> and matrix commands. Additionally, useful tcl commands to know/read up on
> are things like glob, expr, and the list-related commands. I often will
> refer back to https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2Fwww.tcl.tk%2Fman%2Ftcl%2FTclCmd%2Fcontents.htm&data=02%7C01%
> 7Csnw42%40drexel.edu%7C5c2434391fd84f23ac4008d520b394ae%
> 7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C636450878022113423&sdata=
> IRYnIC42wio2RpfqIN0vQnd%2BHiqBMiS81rvo6RoHswU%3D&reserved=0.
>
> Happy coding!
>
> -Josh Vermaas
>
> On 10/31/2017 04:17 PM, Windle,Stephen wrote:
>
> VMD Users,
>
>
> Good afternoon. I am very new to the VMD software, and I am working on
> putting together a script for a specific purpose, but I am unsure how much
> of it can be done as a single script. Essentially, I want to measure the
> distances between all the side chains of a specific amino acid in a given
> protein (for example distances between all the valine side chains).
> However, I want to be able to load anywhere from 1000-10,000 molecules into
> VMD and have the script do this for each molecule consecutively, exporting
> them into individual files (I should be able to write a loop for this, I
> imagine). So far I'm able to load a molecule and isolate the side chains of
> a specific amino acid. So my two key questions are this: Can a loop be
> written to load every .pdb file in a given folder, and what are the console
> commands to measure the distance between each side chain once they've been
> isolated into a named selection. I have tried searching through the indexed
> messages but to no avail. If someone could point me in the right direction
> that would be greatly appreciated. Thank you!
>
>
> Regards,
>
> Steve Windle
>
>