[chimerax-users] Select ring atoms of ligand using python in chimerax

[Dr. Vijay Masand]

Thank you for the details and nice solution, Eric.
How can I extend the above code to select ring nitrogen and oxygen atoms
and to sum charges on different atoms (ring/non-ring)?
Thanks in advance.

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/



On Wed, Jan 18, 2023 at 1:36 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Vijay,
> I don't know exactly how efficient you need things to be, but here is some
> info...
>
> *Get all atoms*:
> from chimerax.atomic import all_atoms
> atoms = all_atoms(session)
>
> *Filter down to just ligand atoms*:
> ligand_atoms = atoms.filter(atoms.structure_categories == "ligand")
>
> *Ligand ring atoms*:
> ring_atoms = [a for a in ligand_atoms if a.rings()]
>
> *Assign charges to ligand residues*:
> from chimerax.add_charge import add_charges
> add_charges(session, ligand_atoms.unique_residues)
>
> *Sum the charges*:
> charge_sum = sum([a.charge for a in ligand_atoms])
>
> This all assumes the structure has hydrogens.  In particular, the charge
> sum will be massively negative if hydrogens are missing!  Some of the calls
> above are covered in the ChimeraX programmer's guide (
> https://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html, also included
> in the app under Help), particularly the "API Reference" link.
> When you said "select ring atoms" I don't know if you meant just find them
> (which the above does) or actually select them in the graphics window.
> This would do that:
>
> session.selection.clear()
> for a in ring_atoms:
> a.selected = True
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Jan 16, 2023, at 11:03 PM, Dr. Vijay Masand via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear all
> I am looking for an efficient method to select ring atoms of ligands using
> python in chimeraX. Also, is there any python code/method to get the sum of
> charges on ligand atoms only?
> Thanks in advance.
> From
> Vijay
>
> With Warm Regards
> *Dr. Vijay H. Masand*
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
>
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