VMD-L Mailing List

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Thu Oct 11 2018 - 02:54:11 CDT

Hi kelly, I think Dr. Fiorin meant something like this:

# measure the dihedral and save to output
 for { set frame 0 } { $frame < $ntot } { incr frame } {
 foreach c [list 1 2 3 4] {
 set x [measure dihed "$dihe0($c)" frame $frame ]
 lappend xdihe$c $x
 }
 foreach c1 $xdihe1 c2 $xdihe2 c3 $xdihe3 c4 $xdihe4 {
  puts $outdid [format "%.4f %.4f %.4f %.4f" $c1 $c2 $c3 $c4]
}
}

Regards,
Souvik

On Thu, Oct 11, 2018 at 6:15 AM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> Could that be done within this script, where would the foreach loop and
> format be placed?:
>
>
> # input
> set input1 Simulation_QwikMD
> set input2 win8-1
> mol load psf $input1.psf dcd $input2.dcd
>
> # output
> set outdi "../Dihedrals/win8-1.dat"
> set outdiid [open $outdi "w"]
>
> # write header
> #set headdi "# frame ASP44-1 ASP44-2 ASP44-3 ASP44-4 TRP41-1 TRP41-2
> TRP41-3 TRP41-4 HIS37-1 HIS37-2 #HIS37-3 HIS37-4 SER31-1 SER31-2 SER31-3
> SER31-4 VAL27-1 VAL27-2 VAL27-3 VAL27-4"
> #puts $outdiid $headdi
>
> # atom selection
> set dihe01 [[atomselect top "segname PP1 and (name N CA CB CG1) and
> resname VAL and resid 27"] get index]
>
> set dihe02 [[atomselect top "segname PP2 and (name N CA CB CG1) and
> resname VAL and resid 27"] get index]
>
> set dihe03 [[atomselect top "segname PP3 and (name N CA CB CG1) and
> resname VAL and resid 27"] get index]
>
> set dihe04 [[atomselect top "segname PP4 and (name N CA CB CG1) and
> resname VAL and resid 27"] get index]
>
> # obtain total number of frames
> set ntot [molinfo top get numframes]
>
> # measure the dihedral and save to output
> for { set frame 0 } { $frame < $ntot } { incr frame } {
> set xdihe01 [measure dihed "$dihe01" frame $frame ]
> puts $outdiid VAL27PP1\t$xdihe01
> }
>
> for { set frame 0 } { $frame < $ntot } { incr frame } {
> set xdihe02 [measure dihed "$dihe02" frame $frame ]
> puts $outdiid VAL27PP2\t$xdihe02
> }
>
> for { set frame 0 } { $frame < $ntot } { incr frame } {
> set xdihe03 [measure dihed "$dihe03" frame $frame ]
> puts $outdiid VAL27PP3\t$xdihe03
> }
>
> for { set frame 0 } { $frame < $ntot } { incr frame } {
> set xdihe04 [measure dihed "$dihe04" frame $frame ]
> puts $outdiid VAL27PP4\t$xdihe04
> }
>
> # close output
> close $outdiid
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> *Sent:* Wednesday, October 10, 2018 2:19:05 PM
> *To:* McGuire, Kelly
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: VMD Tk Console Columns
>
> Hi Kelly, you could use a "foreach" loop to iterate over the four lists,
> and the "format" command to print the four values in a specific arrangement.
> https://tcl.tk/man/tcl8.5/TclCmd/contents.htm
>
> Giacomo
>
> On Wed, Oct 10, 2018 at 4:05 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
> I am writing dihedrals of 4 sidechains from a trajectory. Everything
> works great, except I would like to write the four lists of dihedrals in
> separate columns instead of on long list. How do I write separate columns
> spaced and next to each other? Thanks!
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
> 

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275