From: Branko (
Date: Wed Nov 10 2010 - 11:50:30 CST


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 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

#set outfile "rgyrA"
#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<> 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.