From: Peter Freddolino (
Date: Tue Jan 23 2007 - 10:10:59 CST

Dear Regina,
you can do this from the gui by clicking on your molecule of interest,
choosing File-->Save coordinates, and then choosing an appropriate frame
range and selection. This can be done through the tcl interface using
the animate writepdb command.

" politr" wrote:
> I want all the frames to be appended to the same pdb file separated by
> lets say "ENDMDL"
> Thanks
> -------- Original Message --------
> Subject: pdb from trajectory
> Date: Tue, 23 Jan 2007 17:16:29 +0200
> From:
> Organization: Fritz Haber Research Center
> To:
> Dear VMD users and developers,
> I have a trajectory of protein in a water box. I have loaded this
> trajectory in a VMD and I'm interested to create pdb file of my protein
> from every frame of the trajectory. What I mean is, to create tcl script
> that will save only my protein from every frame in a pdb format. Can
> someone help me with this issue? Any help is more than appreciated.
> Thank you very much
> Regina