Re: [PyMOL] How to select nucleic/protein separately

[Tony L. <ton...@gm...>]

Hi Thomas,

Thanks very much for your reply. That's really helpful - your suggestion
looks much better than the resn command I was previously using.

Kind regards,

Tony Lewis


On 7 December 2017 at 09:02, Thomas Holder <tho...@sc...>
wrote:

> Hi Tony,
>
> Unfortunately, PyMOL knows only temporarily during cartoon generation
> what's protein and what's nucleic acid. It doesn't store this information
> with the atoms.
>
> Maybe the following is a more robust hack than using residue names:
>
> select protein, (byres polymer & name CA)
> select nucleic, (byres polymer & name P)
> select rna, (byres polymer & name O2')
> select dna, (nucleic & !rna)
>
> To update these selections with a single key press, put this in your
> pymolrc:
>
> set_key F1, \
>   select protein, (byres polymer & name CA) \
>   select nucleic, (byres polymer & name P) \
>   select rna, (byres polymer & name O2') \
>   select dna, (nucleic & !rna)
>
> Cheers,
>   Thomas
>
> > On Nov 30, 2017, at 1:00 PM, Tony Lewis <ton...@gm...> wrote:
> >
> > Dear PyMOL people,
> >
> > Please can anyone tell me if there's a standard way to select either of
> nucleic / protein separately?
> >
> > I can use `polymer` to get both together but I can't see a standard way
> to distinguish nucleic / protein within that.
> >
> > I'm currently using something like `resn A+C+G+U+DA+DC+DG+DT` to
> identify nucleic but that's inadequate because it misses out various resn
> values (eg BRU, OMG etc) that are part of modified DNA/RNA.
> >
> > The thing is: PyMOL clearly *knows* which bits are protein versus
> nucleic because it draws the cartoons accordingly. So it feels like I
> should be accessing this info from PyMOL rather than trying to hack
> together a list of resn values.
> >
> > Many thanks for any help.
> >
> > Tony Lewis
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>