From: Philip Fowler (
Date: Mon Mar 22 2004 - 02:42:02 CST

> I am relatively new to VMD and I am already a big fan of its powerful and
> vast tools. Currently, I am writing a tcl script to align the frames of an
> animation using rmsd. As an intermediate step, I need to take a frame of
> an animation and make a copy of it so that I can proceed with my work on
> that copy without affecting what happens to the original frame that it is
> derived from. Is there a way to copy a selection of all of the atoms of a
> frame, or just the frame itself to a new location? For reference, this is
> the way I select the frame (using tcl):
> set sel [atomselect $mol $seltext frame $j]

Hi Adam,

Probably the easiest thing is to use your selection to write a PDB file which
you may then load back into VMD. If you have a PSF topology file for your DCD
trajectory file, then it will work also for this PDB, if you are not using
one, don't worry. The syntax is

> set sel [atomselect $mol $seltext frame $j]
> $sel writepdb myfilename.pdb


Philip Fowler, 
PhD Student
Centre for Computational Science,
UCL Chemistry