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

Thu Jan 26 18:19:50 PST 2023

Dear Eric
I also observed the same and then simply added 'return area' after line
number 52. This solved my problem. I am sending the modified
'measure_sasacmd.py' file.

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 Fri, Jan 27, 2023 at 7:14 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> I see.  “measure sasa” is only reporting the value in the log and not
> returning it to Python.  I have opened a ticket in our bug-tracking
> database about this with you cc’ed.  Hopefully it will be fixed soon.
>
> —Eric
>
> On Jan 25, 2023, at 10:22 PM, Dr. Vijay Masand via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear Eric,
> I agree with you, but for a specific purpose, I need to know sasa for ring
> atoms only of a ligand. I hope I will get a pythonic way as I have to
> repeat the task for multiple ligands simultaneously. Thanks in advance.
>
>
> On Thu, 26 Jan, 2023, 00:30 Eric Pettersen, <pett at cgl.ucsf.edu> wrote:
>
>> Hi Vijay,
>> Do you really mean to use 'all' as the first atom spec for "measure
>> sasa"?  If the ligand is buried in a receptor pocket, the surface will
>> enclose the entire system and the SASA of many of the ring atoms will
>> probably be zero.  I would think you would want to use 'ligand' instead of
>> 'all'.
>>
>> --Eric
>>
>> On Jan 25, 2023, at 6:48 AM, Dr. Vijay Masand via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Thank you, Eric. The above commands are very helpful.
>> Using following command, I am getting sasa for all Carbon atoms:
>> from chimerax.core.commands import run as rc
>> from chimerax.atomic import all_atoms
>> atoms = all_atoms(session)
>>         ring_atoms = [a for a in atoms if a.rings()]
>>         ringC = [a for a in ring_atoms if a.element.name == "C"]
>>        for a in ringC:
>>         SASA = rc(session, 'measure sasa all sum %s'%a)
>>         print(SASA)
>> But I am not getting the expected result. I am now looking for a better
>> pythonic way to calculate sasa for ring carbon atoms of ligand only.
>> Thanks in advance for the help.
>>
>> 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 Thu, Jan 19, 2023 at 12:39 AM Eric Pettersen <pett at cgl.ucsf.edu>
>> wrote:
>>
>>> Hi Vijay,
>>> Atom objects have an 'element' attribute which in turn has 'name' and
>>> 'number' attributes.  The 'name' attribute is actually the atomic symbol,
>>> *e.g.* H for hydrogen.
>>> You can use normal Python operations, such as 'not', to find these
>>> things, so the non-ring ligand atoms are: [a for a in ligand_atoms if not
>>> a.rings()]
>>>
>>> --Eric
>>>
>>> On Jan 17, 2023, at 6:26 PM, Dr. Vijay Masand via ChimeraX-users <
>>> chimerax-users at cgl.ucsf.edu> wrote:
>>>
>>> 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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