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

Thu Jan 26 17:44:36 PST 2023

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 <mailto: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 <mailto: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 <http://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/ <https://sites.google.com/site/vijaymasand/>
>> 
>> 
>> 
>> On Thu, Jan 19, 2023 at 12:39 AM Eric Pettersen <pett at cgl.ucsf.edu <mailto: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 <mailto: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/ <https://sites.google.com/site/vijaymasand/>
>>> 
>>> 
>>> 
>>> On Wed, Jan 18, 2023 at 1:36 AM Eric Pettersen <pett at cgl.ucsf.edu <mailto: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 <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 <mailto: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/ <https://sites.google.com/site/vijaymasand/>
>>>> 
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