Select ring atoms of ligand using python in chimerax
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/
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@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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@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@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@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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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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@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@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@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@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@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@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/
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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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Hi Vijay,
I made "measure sasa" in the daily build return the area of the atoms and sum atoms.
total_area, sum_area = runCommand(session, 'measure sasa #1 sum :15')
If you don't specify the "sum" option then it just returns the total area. This will be in tomorrow's ChimeraX daily build dated January 27.
Tom
On Jan 26, 2023, at 5:44 PM, Eric Pettersen via ChimeraX-users chimerax-users@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@cgl.ucsf.edu mailto:chimerax-users@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@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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/
On Thu, Jan 19, 2023 at 12:39 AM Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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@cgl.ucsf.edu mailto:pett@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@cgl.ucsf.edu mailto:chimerax-users@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/ >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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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@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@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@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@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@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@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@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@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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participants (3)
-
Dr. Vijay Masand -
Eric Pettersen -
Tom Goddard