CONECT records are not used for peptide bonds for standard amino acid and
nucleic acid links. These are assumed. In addition, for these standard
chemical component, CONECT records are not used to internal bonds - they
are "known."
Non standard amino/nucleic acids used CONECT records for all atoms present.
On Tue, Jan 19, 2016 at 5:48 PM, David Hall <li...@cowsandmilk.net> wrote:
> 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 <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 <lahue...@uv.es>>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net <
> mailto:PyMOL-users@lists.sourceforge.net
> <PyMOL-users@lists.sourceforge.net>>)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
