Hi Edward,
Oh, I read over the moving part. Well, what I meant to convey is that you
can use CONECT records to draw additional bonds, but for the rest
bondedness is inferred from distance. So you can only remove bonds if the
particles are further apart than the cutoff AND have a CONECT record.
But moving and saving is possible ofcourse. There's the possibility to edit
wit the mouse and you can use commands alter_state, translate and rotate.
To save the new coordinates, well... use 'save'.
Hope it helps,
Tsjerk
On Jan 19, 2016 22:59, "Edward A. Berry" <ber...@upstate.edu> wrote:
>
>
> On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
>
>> 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,
>>
>
> (Actually of course the PDB file format does (or did) have a way to specify
> bonds, but i guess no programs ever used it)
> But the poster did specify moving atoms (to) break bonds and separate
> atoms,
> so maybe that is where the help is needed- how do you move atoms in Pymol?
> Or since this is probably a RTFM-type question, perhaps a pointer
> to chapter and verse in the wiki would be more appropriate?
> And then to save the modified pdb: I suppose file:save:molecule, and
> it will be obvious which molecule to save?
>
>>
>> Tsjerk
>>
>> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta <
>> pascual.lahue...@uv.es <mailto: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 <mailto:lahue...@uv.es>
>>
>>
>>
>>
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>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>>
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