Hi Michael, Have you had a look at 'help selections'?
> I am wondering how to select molecules in Pymol. What exactly do you mean here? The molecule for a certain atom? The molecule as in 'chain' (if it's a macromolecule), or as in 'residue' (if it's a ligand/cofactor/solvent)? > The system I am studying has an amide of interest (oleamide) in oil (At > the moment just dodecane molecules). > I have seen in the manual how to select individual elements, but is it > possible to select either the Nitrogen or oxygen in my oleamide > molecules, and then select all atoms which are bonded to this to > therefore select the entire oleamide molecule. Now, either/or sort of suggests logical XOR (exclusive or), which would mean nitrogen if only nitrogen is present (and not oxygen), oxygen if only oxygen is present (and not nitrogen), and none if none or both are present. But somehow logical XOR with such selections is not that logical to me. Do you want to have all atoms bonded to nitrogen or to oxygen (and assuming you don't have azides, peroxides and nitroxides of interest), then you'd probably want to do something like: select mysele, (not (e. n,o)) within 0.2 of (e. n,o) > Or is it possible to define a molecule by defining a chain of elements > (e.g. define a C12H36 chain for dodecane). I have tried just using the > mouse to select individual molecules but find it very difficult to do > depending on where in my system a particular molecule is. If you're dodecane molecules have unique residue ids than it should be trivial to use those: color yellow, resi 1 If this wasn't what you were after, please restate your question, clearly explaining what you want, what you tried and how that didn't do what you expected. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
