Hi Pascual,
The PDB file does not really have information on bonds. If atoms are closer
than some cutoff a bond is drawn. Unbonding and saving will not change the
distance, so the bond will be drawn again when loaded again. What is your
aim?
Cheers,
Tsjerk
On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta <pascual.lahue...@uv.es>
wrote:
> I am new user of Pymol and I would like to use this program for a very
> simple task that I describe here in three steps:
>
> 1. Start with a simple structure (structure 1.pdb1) either loaded or
> created with the editor.
> 2. The second task will be to change the position of the atoms in
> structure 1, breaking bonds and separating atoms.
> 3. The third step will be to save the resulting structure as
> structure2.pdb file.
>
> I wonder if pymol allows me to perform this task. iI hope someone can
> guide me in this task.
>
> Thanks in advance
>
> Pascual
> =========
>
>
> Pascual Lahuerta
> Universitat de Valencia
> Dep. Q. Inorganica
> Edificio Investigación 3.36
> Dr. Moliner 50
> 46100 Burjassot-Valencia
> Despacho 96 354 3147
> Movil 617 188 331
> lahue...@uv.es
>
>
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
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