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> > > > > > ------------------------------------------------------------------------------ > 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>) > 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
