Well, yes, programs do use the CONECT records, including pymol
http://pymolwiki.org/index.php/Connect_mode
Removing bonds is http://pymolwiki.org/index.php/Unbond
Atoms can be translated using the command line
http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python
Or in edit mode
http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move
And then save http://pymolwiki.org/index.php/Save
But honestly, the description sounds like something that would be infinitely
easier to do using some plain python code rather than in pymol.
-David
> On Jan 19, 2016, at 4:59 PM, 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> <mailto: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> <mailto:lahue...@uv.es
>> <mailto:lahue...@uv.es>>
>>
>>
>>
>>
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>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>>
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