VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 23 2007 - 13:45:07 CST

Hi,
  If you want a very specific PDB construction, you could write a script
to emit the frames one at a time, and then use Tcl I/O commands to
concatenate them yourself, which would allow you to control what records
are written between structures if you like. By default, the records
placed between emitted structures are "END" at present. Your script
can tack on "MDL" while concatenating the files.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 23, 2007 at 05:41:49PM +0200, " politr"@huji.ac.il 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: politr_at_huji.ac.il
> Organization: Fritz Haber Research Center
> To: vmd-l_at_ks.uiuc.edu
>
>
>
> 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
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078