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
|
