reduce2 and cell construction from python script

newer
getting indices of selected grid...

Enrico Ravera

13 Feb 2025 13 Feb '25

3:12 a.m.

Hi, I apologize for the naive post. I am trying to figure out how to perform the following tasks: 1) read in a mmcif file (which I think I can do following the tutorial); 2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial); 3) run reduce2 to get hydrogens in the nuclear positions (no clue); 4) get the full content of the unit cell (no clue). Any help is appreciated. All the best, Enrico

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Pavel Afonine

13 Feb 13 Feb

11:42 a.m.

Enrico, here are the steps (check for typos as I was typing all the below from memory):

...

1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

...

2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial);

model_no_H = model.remove_hydrogens() model_no_water = model.remove_solvent() though better: selection = model.selection("not (element H or element D or water)") model_trimmed = model.select(selection)

...

3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H. Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

...

4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then hierarchy = model.get_hierarchy().expand_to_p1() Happy to answer questions! Pavel

Enrico Ravera

1:55 p.m.

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif Any clues? Cheers, E. Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine ha scritto:

...

Enrico,

here are the steps (check for typos as I was typing all the below from memory):

...
1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

...
2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

...
3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

...
4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

Pavel Afonine

1:57 p.m.

Hi Enrico, CC Oleg I hope Oleg can comment on this. Pavel On 2/13/25 13:55, Enrico Ravera wrote:

...

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine ha scritto:

Enrico,

here are the steps (check for typos as I was typing all the below from memory):

> 1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

> 2) trim the solvent and hydrogen atoms (probably I can do it following > the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

> 3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

> 4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

Pavel Afonine

2:08 p.m.

Hi Enrico, this works for me: phenix.fetch_pdb 2gim phenix.model_statistics 2gim.cif mmtbx.reduce2 2gim.cif Something must be lost in communication. Can you provide complete set of steps that lead to the crash? Pavel On 2/13/25 13:55, Enrico Ravera wrote:

...

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine ha scritto:

Enrico,

here are the steps (check for typos as I was typing all the below from memory):

> 1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

> 2) trim the solvent and hydrogen atoms (probably I can do it following > the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

> 3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

> 4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

Enrico Ravera

2:14 p.m.

import sys from iotbx import pdb as pdb from mmtbx import model as mdl from mmtbx.command_line import reduce2 # Load the mmcif file model_filename = sys.argv[1] # Get the model file name from the command line protein = pdb.input(file_name=model_filename) # Load the model model = mdl.manager(model_input=protein) # Create the model manager #trim hidrogen atoms and solvent model_no_H = model.remove_hydrogens() # Remove hydrogen atoms model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent # add hydrogens using reduce in nuclear position model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') # Add hydrogens hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get the hierarchy Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine ha scritto:

...

Hi Enrico,

this works for me:

phenix.fetch_pdb 2gim

phenix.model_statistics 2gim.cif

mmtbx.reduce2 2gim.cif

Something must be lost in communication. Can you provide complete set of steps that lead to the crash?

Pavel On 2/13/25 13:55, Enrico Ravera wrote:

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine ha scritto:

...
Enrico,

here are the steps (check for typos as I was typing all the below from memory):

...
1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

...
2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

...
3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

...
4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

Billy Poon

2:40 p.m.

Hi Enrico, Do you have chem_data or access to some restraints library? It looks like you are using the conda version of cctbx which does not have any restraints. You can get a recent version of chem_data as a conda package here https://cci.lbl.gov/~bkpoon/chem_data-2.0rc1.5606-pyh507b02e_0.conda Download the file and then in your active conda environment with cctbx, run conda install chem_data-2.0rc1.5606-pyh507b02e_0.conda I can confirm that with a newly created cctbx conda environment, mmtbx.reduce2 2gim.cif will fail. After installing chem_data, that command works. We may have to start providing the chem_data conda package on the cctbx GitHub release pages. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Thu, Feb 13, 2025 at 2:14 PM Enrico Ravera wrote:

...

import sys from iotbx import pdb as pdb from mmtbx import model as mdl from mmtbx.command_line import reduce2

# Load the mmcif file model_filename = sys.argv[1] # Get the model file name from the command line protein = pdb.input(file_name=model_filename) # Load the model model = mdl.manager(model_input=protein) # Create the model manager #trim hidrogen atoms and solvent model_no_H = model.remove_hydrogens() # Remove hydrogen atoms model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent # add hydrogens using reduce in nuclear position model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') # Add hydrogens hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get the hierarchy

Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine ha scritto:

...
Hi Enrico,

this works for me:

phenix.fetch_pdb 2gim

phenix.model_statistics 2gim.cif

mmtbx.reduce2 2gim.cif

Something must be lost in communication. Can you provide complete set of steps that lead to the crash?

Pavel On 2/13/25 13:55, Enrico Ravera wrote:

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine ha scritto:

...
Enrico,

here are the steps (check for typos as I was typing all the below from memory):

...
1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

...
2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

...
3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

...
4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

Enrico Ravera

2:48 p.m.

Hi Billy, hi all, I had set the environment variable for CCP4 (it is a new pc, and I did not have phenix installed yet), but getting chem_data solved the problem. I still have to figure out the next steps to saving the files, but for today I am happy, many thanks for your help! All the best, Enrico Il giorno gio 13 feb 2025 alle ore 23:40 Billy Poon ha scritto:

...

Hi Enrico,

Do you have chem_data or access to some restraints library? It looks like you are using the conda version of cctbx which does not have any restraints.

You can get a recent version of chem_data as a conda package here

https://cci.lbl.gov/~bkpoon/chem_data-2.0rc1.5606-pyh507b02e_0.conda

Download the file and then in your active conda environment with cctbx, run

conda install chem_data-2.0rc1.5606-pyh507b02e_0.conda

I can confirm that with a newly created cctbx conda environment,

mmtbx.reduce2 2gim.cif

will fail. After installing chem_data, that command works.

We may have to start providing the chem_data conda package on the cctbx GitHub release pages.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Thu, Feb 13, 2025 at 2:14 PM Enrico Ravera wrote:

...
import sys from iotbx import pdb as pdb from mmtbx import model as mdl from mmtbx.command_line import reduce2

# Load the mmcif file model_filename = sys.argv[1] # Get the model file name from the command line protein = pdb.input(file_name=model_filename) # Load the model model = mdl.manager(model_input=protein) # Create the model manager #trim hidrogen atoms and solvent model_no_H = model.remove_hydrogens() # Remove hydrogen atoms model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent # add hydrogens using reduce in nuclear position model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') # Add hydrogens hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get the hierarchy

Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine ha scritto:

...
Hi Enrico,

this works for me:

phenix.fetch_pdb 2gim

phenix.model_statistics 2gim.cif

mmtbx.reduce2 2gim.cif

Something must be lost in communication. Can you provide complete set of steps that lead to the crash?

Pavel On 2/13/25 13:55, Enrico Ravera wrote:

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine ha scritto:

...
Enrico,

here are the steps (check for typos as I was typing all the below from memory):

...
1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

...
2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

...
3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

...
4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

Pavel Afonine

2:52 p.m.

Hi All, I'm attaching the script the way I'd write it and that works for me. Pavel On 2/13/25 14:48, Enrico Ravera wrote:

...

Hi Billy, hi all, I had set the environment variable for CCP4 (it is a new pc, and I did not have phenix installed yet), but getting chem_data solved the problem. I still have to figure out the next steps to saving the files, but for today I am happy, many thanks for your help! All the best,

Enrico

Il giorno gio 13 feb 2025 alle ore 23:40 Billy Poon ha scritto:

Hi Enrico,

Do you have chem_data or access to some restraints library? It looks like you are using the conda version of cctbx which does not have any restraints.

You can get a recent version of chem_data as a conda package here

https://cci.lbl.gov/~bkpoon/chem_data-2.0rc1.5606-pyh507b02e_0.conda

Download the file and then in your active conda environment with cctbx, run

conda install chem_data-2.0rc1.5606-pyh507b02e_0.conda

I can confirm that with a newly created cctbx conda environment,

mmtbx.reduce2 2gim.cif

will fail. After installing chem_data, that command works.

We may have to start providing the chem_data conda package on the cctbx GitHub release pages.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Thu, Feb 13, 2025 at 2:14 PM Enrico Ravera wrote:

import sys from iotbx import pdb as pdb from mmtbx import model as mdl from mmtbx.command_line import reduce2

# Load the mmcif file model_filename = sys.argv[1] # Get the model file name from the command line protein = pdb.input(file_name=model_filename) # Load the model model = mdl.manager(model_input=protein) # Create the model manager #trim hidrogen atoms and solvent model_no_H = model.remove_hydrogens() # Remove hydrogen atoms model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent # add hydrogens using reduce in nuclear position model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') # Add hydrogens hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get the hierarchy

Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine ha scritto:

Hi Enrico,

this works for me:

phenix.fetch_pdb 2gim

phenix.model_statistics 2gim.cif

mmtbx.reduce2 2gim.cif

Something must be lost in communication. Can you provide complete set of steps that lead to the crash?

Pavel

On 2/13/25 13:55, Enrico Ravera wrote:

...
Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine ha scritto:

Enrico,

here are the steps (check for typos as I was typing all the below from memory):

> 1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

> 2) trim the solvent and hydrogen atoms (probably I can do it following > the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

> 3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

> 4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list [email protected] To unsubscribe send an email [email protected]

Billy Poon

3 p.m.

Hi Enrico, Great! Which environment variable did you set? Was it for CCP4 or for Phenix? We should be checking some variables for restraints locations. And our next cctbx conda package release is at the end of this month, so I'll add a chem_data package to the release since some tools do require restraints. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Thu, Feb 13, 2025 at 2:52 PM Pavel Afonine wrote:

...

Hi All,

I'm attaching the script the way I'd write it and that works for me.

Pavel On 2/13/25 14:48, Enrico Ravera wrote:

Hi Billy, hi all, I had set the environment variable for CCP4 (it is a new pc, and I did not have phenix installed yet), but getting chem_data solved the problem. I still have to figure out the next steps to saving the files, but for today I am happy, many thanks for your help! All the best,

Enrico

Il giorno gio 13 feb 2025 alle ore 23:40 Billy Poon ha scritto:

...
Hi Enrico,

Do you have chem_data or access to some restraints library? It looks like you are using the conda version of cctbx which does not have any restraints.

You can get a recent version of chem_data as a conda package here

https://cci.lbl.gov/~bkpoon/chem_data-2.0rc1.5606-pyh507b02e_0.conda

Download the file and then in your active conda environment with cctbx, run

conda install chem_data-2.0rc1.5606-pyh507b02e_0.conda

I can confirm that with a newly created cctbx conda environment,

mmtbx.reduce2 2gim.cif

will fail. After installing chem_data, that command works.

We may have to start providing the chem_data conda package on the cctbx GitHub release pages.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Thu, Feb 13, 2025 at 2:14 PM Enrico Ravera wrote:

...
import sys from iotbx import pdb as pdb from mmtbx import model as mdl from mmtbx.command_line import reduce2

# Load the mmcif file model_filename = sys.argv[1] # Get the model file name from the command line protein = pdb.input(file_name=model_filename) # Load the model model = mdl.manager(model_input=protein) # Create the model manager #trim hidrogen atoms and solvent model_no_H = model.remove_hydrogens() # Remove hydrogen atoms model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent # add hydrogens using reduce in nuclear position model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') # Add hydrogens hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get the hierarchy

Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine ha scritto:

...
Hi Enrico,

this works for me:

phenix.fetch_pdb 2gim

phenix.model_statistics 2gim.cif

mmtbx.reduce2 2gim.cif

Something must be lost in communication. Can you provide complete set of steps that lead to the crash?

Pavel On 2/13/25 13:55, Enrico Ravera wrote:

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine < [email protected]> ha scritto:

...
Enrico,

here are the steps (check for typos as I was typing all the below from memory):

...
1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

...
2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

...
3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

...
4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

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Enrico Ravera

14 Feb 14 Feb

5:34 a.m.

Hi all, sorry for the delay but first I had to sleep and then to teach. @Pavel, yes, the script works like a charm. @Billy, I had set the CLIBD_MON through the ccp4.setup script, but I had not finished install phenix yet. The $MMTBX_CCP4_MONOMER_LIB environmental variable has not been set by the phenix setup, but I guess this is not necessary. Many thanks again, I will hopefully come up with new questions sometimes in the future. Cheers, E. Il giorno ven 14 feb 2025 alle ore 00:01 Billy Poon ha scritto:

...

Hi Enrico,

Great! Which environment variable did you set? Was it for CCP4 or for Phenix? We should be checking some variables for restraints locations.

And our next cctbx conda package release is at the end of this month, so I'll add a chem_data package to the release since some tools do require restraints.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Thu, Feb 13, 2025 at 2:52 PM Pavel Afonine wrote:

...
Hi All,

I'm attaching the script the way I'd write it and that works for me.

Pavel On 2/13/25 14:48, Enrico Ravera wrote:

Hi Billy, hi all, I had set the environment variable for CCP4 (it is a new pc, and I did not have phenix installed yet), but getting chem_data solved the problem. I still have to figure out the next steps to saving the files, but for today I am happy, many thanks for your help! All the best,

Enrico

Il giorno gio 13 feb 2025 alle ore 23:40 Billy Poon ha scritto:

...
Hi Enrico,

Do you have chem_data or access to some restraints library? It looks like you are using the conda version of cctbx which does not have any restraints.

You can get a recent version of chem_data as a conda package here

https://cci.lbl.gov/~bkpoon/chem_data-2.0rc1.5606-pyh507b02e_0.conda

Download the file and then in your active conda environment with cctbx, run

conda install chem_data-2.0rc1.5606-pyh507b02e_0.conda

I can confirm that with a newly created cctbx conda environment,

mmtbx.reduce2 2gim.cif

will fail. After installing chem_data, that command works.

We may have to start providing the chem_data conda package on the cctbx GitHub release pages.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Thu, Feb 13, 2025 at 2:14 PM Enrico Ravera wrote:

...
import sys from iotbx import pdb as pdb from mmtbx import model as mdl from mmtbx.command_line import reduce2

# Load the mmcif file model_filename = sys.argv[1] # Get the model file name from the command line protein = pdb.input(file_name=model_filename) # Load the model model = mdl.manager(model_input=protein) # Create the model manager #trim hidrogen atoms and solvent model_no_H = model.remove_hydrogens() # Remove hydrogen atoms model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent # add hydrogens using reduce in nuclear position model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') # Add hydrogens hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get the hierarchy

Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine < [email protected]> ha scritto:

...
Hi Enrico,

this works for me:

phenix.fetch_pdb 2gim

phenix.model_statistics 2gim.cif

mmtbx.reduce2 2gim.cif

Something must be lost in communication. Can you provide complete set of steps that lead to the crash?

Pavel On 2/13/25 13:55, Enrico Ravera wrote:

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine < [email protected]> ha scritto:

...
Enrico,

here are the steps (check for typos as I was typing all the below from memory):

> 1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

> 2) trim the solvent and hydrogen atoms (probably I can do it following > the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

> 3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

> 4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

Son Kenneth

6 Jun 6 Jun

3:50 p.m.

hello On Fri, Feb 14, 2025, 2:35 PM Enrico Ravera wrote:

...

Hi all, sorry for the delay but first I had to sleep and then to teach. @Pavel, yes, the script works like a charm. @Billy, I had set the CLIBD_MON through the ccp4.setup script, but I had not finished install phenix yet. The $MMTBX_CCP4_MONOMER_LIB environmental variable has not been set by the phenix setup, but I guess this is not necessary.

Many thanks again, I will hopefully come up with new questions sometimes in the future.

Cheers,

E.

Il giorno ven 14 feb 2025 alle ore 00:01 Billy Poon ha scritto:

...
Hi Enrico,

Great! Which environment variable did you set? Was it for CCP4 or for Phenix? We should be checking some variables for restraints locations.

And our next cctbx conda package release is at the end of this month, so I'll add a chem_data package to the release since some tools do require restraints.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road https://www.google.com/maps/search/1+Cyclotron+Road?entry=gmail&source=g, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Thu, Feb 13, 2025 at 2:52 PM Pavel Afonine wrote:

...
Hi All,

I'm attaching the script the way I'd write it and that works for me.

Pavel On 2/13/25 14:48, Enrico Ravera wrote:

Hi Billy, hi all, I had set the environment variable for CCP4 (it is a new pc, and I did not have phenix installed yet), but getting chem_data solved the problem. I still have to figure out the next steps to saving the files, but for today I am happy, many thanks for your help! All the best,

Enrico

Il giorno gio 13 feb 2025 alle ore 23:40 Billy Poon ha scritto:

...
Hi Enrico,

Do you have chem_data or access to some restraints library? It looks like you are using the conda version of cctbx which does not have any restraints.

You can get a recent version of chem_data as a conda package here

https://cci.lbl.gov/~bkpoon/chem_data-2.0rc1.5606-pyh507b02e_0.conda

Download the file and then in your active conda environment with cctbx, run

conda install chem_data-2.0rc1.5606-pyh507b02e_0.conda

I can confirm that with a newly created cctbx conda environment,

mmtbx.reduce2 2gim.cif

will fail. After installing chem_data, that command works.

We may have to start providing the chem_data conda package on the cctbx GitHub release pages.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road https://www.google.com/maps/search/1+Cyclotron+Road?entry=gmail&source=g, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Thu, Feb 13, 2025 at 2:14 PM Enrico Ravera wrote:

...
import sys from iotbx import pdb as pdb from mmtbx import model as mdl from mmtbx.command_line import reduce2

# Load the mmcif file model_filename = sys.argv[1] # Get the model file name from the command line protein = pdb.input(file_name=model_filename) # Load the model model = mdl.manager(model_input=protein) # Create the model manager #trim hidrogen atoms and solvent model_no_H = model.remove_hydrogens() # Remove hydrogen atoms model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent # add hydrogens using reduce in nuclear position model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') # Add hydrogens hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get the hierarchy

Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine < [email protected]> ha scritto:

...
Hi Enrico,

this works for me:

phenix.fetch_pdb 2gim

phenix.model_statistics 2gim.cif

mmtbx.reduce2 2gim.cif

Something must be lost in communication. Can you provide complete set of steps that lead to the crash?

Pavel On 2/13/25 13:55, Enrico Ravera wrote:

Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine < [email protected]> ha scritto:

> Enrico, > > here are the steps (check for typos as I was typing all the below > from > memory): > > > 1) read in a mmcif file (which I think I can do following the > tutorial); > > pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or > mmCIF > model = mmtbx.model.manager(model_input = pdb_inp) > > > 2) trim the solvent and hydrogen atoms (probably I can do it > following > > the tutorial); > > model_no_H = model.remove_hydrogens() > > model_no_water = model.remove_solvent() > > though better: > > selection = model.selection("not (element H or element D or water)") > > model_trimmed = model.select(selection) > > > 3) run reduce2 to get hydrogens in the nuclear positions (no clue); > > Run > mmtbx.reduce OR > mmtbx.reduce2 OR > mmtbx.hydrogenate > > to add H. I have no idea about the difference between the three > commands > (perhaps just the mess that someone has to finally get brave enough > to > clean!), but all three are supposed to add H. > > Also, you should be able to access the above calls programmatically, > at > Python script level, not running in the CL. > > > 4) get the full content of the unit cell (no clue). > > Do you mean expand to P1 (if original symmetry is not P1)? If so, > then > > hierarchy = model.get_hierarchy().expand_to_p1() > > Happy to answer questions! > Pavel > > _______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

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Pavel Afonine

13 Feb 13 Feb

2:59 p.m.

Hi Enrico, the script that I just sent solves these "problems" (next steps to saving the files etc). Pavel On 2/13/25 14:48, Enrico Ravera wrote:

...

Hi Billy, hi all, I had set the environment variable for CCP4 (it is a new pc, and I did not have phenix installed yet), but getting chem_data solved the problem. I still have to figure out the next steps to saving the files, but for today I am happy, many thanks for your help! All the best,

Enrico

Il giorno gio 13 feb 2025 alle ore 23:40 Billy Poon ha scritto:

Hi Enrico,

Do you have chem_data or access to some restraints library? It looks like you are using the conda version of cctbx which does not have any restraints.

You can get a recent version of chem_data as a conda package here

https://cci.lbl.gov/~bkpoon/chem_data-2.0rc1.5606-pyh507b02e_0.conda

Download the file and then in your active conda environment with cctbx, run

conda install chem_data-2.0rc1.5606-pyh507b02e_0.conda

I can confirm that with a newly created cctbx conda environment,

mmtbx.reduce2 2gim.cif

will fail. After installing chem_data, that command works.

We may have to start providing the chem_data conda package on the cctbx GitHub release pages.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Thu, Feb 13, 2025 at 2:14 PM Enrico Ravera wrote:

import sys from iotbx import pdb as pdb from mmtbx import model as mdl from mmtbx.command_line import reduce2

# Load the mmcif file model_filename = sys.argv[1] # Get the model file name from the command line protein = pdb.input(file_name=model_filename) # Load the model model = mdl.manager(model_input=protein) # Create the model manager #trim hidrogen atoms and solvent model_no_H = model.remove_hydrogens() # Remove hydrogen atoms model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent # add hydrogens using reduce in nuclear position model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') # Add hydrogens hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get the hierarchy

Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine ha scritto:

Hi Enrico,

this works for me:

phenix.fetch_pdb 2gim

phenix.model_statistics 2gim.cif

mmtbx.reduce2 2gim.cif

Something must be lost in communication. Can you provide complete set of steps that lead to the crash?

Pavel

On 2/13/25 13:55, Enrico Ravera wrote:

...
Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the following error: File "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", line 1572, in resolve_unexpected mod_mod_id = mod_dict["NH1NOTPRO"] the file i am parsing is https://files.rcsb.org/view/2GIM.cif

Any clues?

Cheers,

E.

Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine ha scritto:

Enrico,

here are the steps (check for typos as I was typing all the below from memory):

> 1) read in a mmcif file (which I think I can do following the tutorial);

pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)

> 2) trim the solvent and hydrogen atoms (probably I can do it following > the tutorial);

model_no_H = model.remove_hydrogens()

model_no_water = model.remove_solvent()

though better:

selection = model.selection("not (element H or element D or water)")

model_trimmed = model.select(selection)

> 3) run reduce2 to get hydrogens in the nuclear positions (no clue);

Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate

to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H.

Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.

> 4) get the full content of the unit cell (no clue).

Do you mean expand to P1 (if original symmetry is not P1)? If so, then

hierarchy = model.get_hierarchy().expand_to_p1()

Happy to answer questions! Pavel

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]

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Billy Poon
Enrico Ravera
Pavel Afonine
Son Kenneth

reduce2 and cell construction from python script

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