extracting coordinates from dcd file

From: M. Madhu (madhu7_at_hotmail.com)
Date: Mon Jul 30 2007 - 13:50:00 CDT


I want to get xyz coordinates for a selected atom from a trajectory (dcd) file.
I have a tcl script for extracting the coordinates from a dcd file, but it does not
give me any values. It gives only blank lines corresponding to the number
of frames. However, if I don't use the loop and do the calculation for a single
pdb file, it works fine.

The following is the tcl script: Could anyone tell me what is wrong with it.


set outfile [open coords.dat w];
mol delete all

mol load mydcdfile.dcd psf mypsffile.psf
set nf [molinfo top get numframes]

# loop
 for {set i 1 } {$i < $nf } { incr i } {
    set sel1 [atomselect top "protein and resid 1 and type CA" frame $i]
    set x1 [$sel1 get x]
    set y1 [$sel1 get y]
    set z1 [$sel1 get z]
    puts $outfile "$x1"
close $outfile
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