VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun Nov 05 2017 - 00:25:41 CDT

Difficult to assess the error without the files for which you are using it.

A guess would be that your selections are not valid. If you select a
residue that doesn't exist, an empty selection can generate this type of
error.

On Nov 5, 2017 11:24, "Windle,Stephen" <snw42_at_drexel.edu> wrote:

> Ok, so, I have 4 proteins loaded, and I've added a for loop to cycle
> through each one and perform the task. However, I am getting an error that
> reads "Bad weight sum: would cause divide by zero." Any advice on what is
> causing this? Here is the script:
>
>
> set x 0
>
> for { set x 0 } { $x < 4 } { incr x } {
>
> set allsel [atomselect $x "sidechain and resname ALA"]
> set residuelist [lsort -unique -integer [$allsel get residue]]
>
> set ressellist [list ]
> foreach residue $residuelist {
> lappend ressellist [atomselect top "residue $residue"]
> }
>
> set file [open "myoutput.txt" w]
>
> set filename $x
>
> for { set i 0 } { $i < [llength $ressellist] } { incr i } {
> for { set j [expr {$i+1}] } { $j < [llength $ressellist] } { incr j } {
> puts $file "$i $j [veclength [vecsub [measure center [lindex $ressellist
> $i]] [measure center [lindex $ressellist $j]]]]"
> }
>
> }
>
>
> close $file
>
> }
>
> Thanks!
> ------------------------------
> *From:* Chitrak Gupta <chgupta_at_mix.wvu.edu>
> *Sent:* Friday, November 3, 2017 7:16:55 PM
> *To:* Windle,Stephen
> *Cc:* Vermaas, Joshua; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Computing atom distances
>
> 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%7C5c2434391fd84f23ac4008d520b39
> 4ae%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C63645087802
> 2113423&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%7C5c2434391fd84f23ac4008d520b39
> 4ae%7C3664e6fa47bd45a696708c4f080f8ca6%7C0%7C0%7C63645087802
> 2113423&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
>
>
>