VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 10 2010 - 12:40:40 CST

branko,

On Wed, Nov 10, 2010 at 12:50 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
>
> Axel,
>
> Thanks for a prompt respond, below are two scripts that I try to use. For
> the first one I receive message that channel for rgyrA is unknown, second

this is due to lack of understanding of basic Tcl file I/O syntax. PEBCAC!

> script only load psf and dcd, but without any analysis. For first script psf
> and dcd were loaded before sourcing and all files are in the same directory.
> As information chosen atoms are always the same in whole trajectory. Thanks
> for help

you don't even have to two scripts.
here is a better variant (untested):

set mol [mol new 4Brintheat.psf type psf waitfor all]
mol addfile 4Brinthdin.dcd type dcd waitfor all
set outfile "rgyrA.dat"

set nf [molinfo $mol get numframes]
set out [open $outfile w]

set sel [atomselect $mol "index 8 to 16 20"]
for { set i 0 } { $i < $nf } {incr i} {
  $sel frame $i
  puts $out "$i [measure rgyr $sel]"
}
$sel delete
close $out

that should do unless i made a typo somewhere.

axel.

> #set col [atomselect top "index 8 to 16 20"]
> #set X [measure rgyr $col]
> #foreach x $X {
>    puts $outfile "$x"
> #}
> #close $outfile
> ---------------------------------------------
> #mol new 4Brintheat.psf
> #mol addfile 4Brinthdin.dcd
> #set a {}
> #set sel [atomselect top "index 8 to 16 20"]
> #for { set i 0 } { $i <=9999 } {incr i} {
>   #$sel frame $i
>   #lappend a [measure rgyr $sel]
> #}
> #$sel delete
>
> Lines were not commented, but I have a problem with the delivery
>
>
> On 11/10/2010 6:12 PM, Axel Kohlmeyer wrote:
>
> On Wed, Nov 10, 2010 at 12:06 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
>
>
> Axel,
>
> Thank you very much for respond. Mater of fact after reading of tcl and vmd
> manual, and  some editing of psf , regular selection can be done and now I
> have $col that include needed atoms, and when I execute measure rgyr $col
> this really works without problem but only for frame on screen, but I need
> rgyr for whole trajectory, every trial to add "frame all" after measure rgyr
> $col result with information that measure rgyr: parameter can only be
> 'weight'.
>
>
> yes. that is the way how measure rgyr is implemented.
> but that is easy to alleviate. just do a loop around all
> frames and then move the selection to the next frame
> with: $col frame $i
> if the selection may contain different atoms in each frame
> (e.g. when you use a "within" in the selection text) then
> you also have to do a: $col update
> to have vmd recompute the selection.
>
> that should do the thing. have a look at the scripting for text mode
> analysis section towards the end of the VMD user's guide for some
> examples. there also should be plenty in the mailing list archives.
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.