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
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
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
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
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
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
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
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
participants (3)
-
Billy Poon -
Enrico Ravera -
Pavel Afonine