Visualization¶

Visualize the best fitted pdb by powerfit with MolStar.

The notebook expects you have run the workflow.ipynb notebook first to generate some results.

This notebook must be executed to see the visualization.

In [1]:

from pathlib import Path

from protein_detective.db import connect, load_fitted_models, load_powerfit_runs

from pathlib import Path from protein_detective.db import connect, load_fitted_models, load_powerfit_runs

In [2]:

import logging

logging.basicConfig(level=logging.INFO)

import logging logging.basicConfig(level=logging.INFO)

In [3]:

session_dir = Path("session1")
session_dir

session_dir = Path("session1") session_dir

Out[3]:

PosixPath('session1')

In [4]:

with connect(session_dir, read_only=True) as conn:
    runs = load_powerfit_runs(conn)
runs

with connect(session_dir, read_only=True) as conn: runs = load_powerfit_runs(conn) runs

INFO:protein_detective.db:Database is in read-only mode, skipping initialization.

Out[4]:

[(1,
  PowerfitOptions(target=PosixPath('../../powerfit-tutorial/ribosome-KsgA.map'), resolution=13.0, angle=20.0, laplace=True, core_weighted=False, no_resampling=False, resampling_rate=2.0, no_trimming=False, trimming_cutoff=None, gpu=False, nproc=1),
  PosixPath('session1/powerfit/1/ribosome-KsgA.map'))]

Use density map from the first run

In [5]:

powerfit_run_id, _options, density_map = runs[0]
powerfit_run_id, density_map

powerfit_run_id, _options, density_map = runs[0] powerfit_run_id, density_map

Out[5]:

(1, PosixPath('session1/powerfit/1/ribosome-KsgA.map'))

The table of solutions of first run.

In [6]:

with connect(session_dir, read_only=True) as conn:
    fitted_models = load_fitted_models(conn)
    fitted_models = fitted_models[fitted_models["powerfit_run_id"] == powerfit_run_id]
fitted_models

with connect(session_dir, read_only=True) as conn: fitted_models = load_fitted_models(conn) fitted_models = fitted_models[fitted_models["powerfit_run_id"] == powerfit_run_id] fitted_models

INFO:protein_detective.db:Database is in read-only mode, skipping initialization.

Out[6]:

	powerfit_run_id	structure	rank	fitted_model_file	unfitted_model_file	cc	fishz	relz	translation	rotation	density_filter_id	af_id	pdb_id	uniprot_acc
0	1	A8MT69_4ne3_B2A	1	session1/powerfit/1/A8MT69_4ne3_B2A/fit_1.pdb	session1/single_chain/A8MT69_4ne3_B2A.pdb	0.429	0.459	10.376	[276.3, 248.67, 153.5]	[0.0, 0.0, 1.0, 0.797, 0.604, 0.0, -0.604, 0.7...	<NA>	None	4NE3	A8MT69
1	1	A8MT69_4ne3_B2A	2	session1/powerfit/1/A8MT69_4ne3_B2A/fit_2.pdb	session1/single_chain/A8MT69_4ne3_B2A.pdb	0.426	0.455	10.289	[227.18, 245.6, 214.9]	[0.0, 0.0, -1.0, 1.0, 0.0, 0.0, 0.0, -1.0, 0.0]	<NA>	None	4NE3	A8MT69
2	1	A8MT69_4ne3_B2A	3	session1/powerfit/1/A8MT69_4ne3_B2A/fit_3.pdb	session1/single_chain/A8MT69_4ne3_B2A.pdb	0.422	0.450	10.167	[138.15, 153.5, 138.15]	[-1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0]	<NA>	None	4NE3	A8MT69
3	1	A8MT69_4ne3_B2A	4	session1/powerfit/1/A8MT69_4ne3_B2A/fit_4.pdb	session1/single_chain/A8MT69_4ne3_B2A.pdb	0.416	0.442	9.999	[141.22, 168.85, 141.22]	[-0.548, -0.816, 0.184, -0.632, 0.548, 0.548, ...	<NA>	None	4NE3	A8MT69
4	1	A8MT69_4ne3_B2A	5	session1/powerfit/1/A8MT69_4ne3_B2A/fit_5.pdb	session1/single_chain/A8MT69_4ne3_B2A.pdb	0.411	0.437	9.883	[227.18, 236.39, 230.25]	[0.816, -0.548, 0.184, 0.184, 0.548, 0.816, -0...	<NA>	None	4NE3	A8MT69

Show top 3 models with density map¶

In [7]:

from protein_detective.visualization import show_fitted_models_and_density

from protein_detective.visualization import show_fitted_models_and_density

In [8]:

show_fitted_models_and_density(
    fitted_models.head(3),
    density_map,
)

show_fitted_models_and_density( fitted_models.head(3), density_map, )

Show best fitted model with density map¶

Pick first and best fitted PDB to visualize

In [9]:

if powerfit_run_id != fitted_models.iloc[0].powerfit_run_id:
    msg = "Run ID does not match the first fitted PDB's run ID."
    raise ValueError(msg)
fitted_model_file = fitted_models.iloc[0].fitted_model_file
fitted_model_file

if powerfit_run_id != fitted_models.iloc[0].powerfit_run_id: msg = "Run ID does not match the first fitted PDB's run ID." raise ValueError(msg) fitted_model_file = fitted_models.iloc[0].fitted_model_file fitted_model_file

Out[9]:

'session1/powerfit/1/A8MT69_4ne3_B2A/fit_1.pdb'

The view object contains the density map data whichi is very large (>10Mb). So it is not executed by default to keep the notebook size small. You can copy the code below to execute it.

from protein_detective.visualization import show_structure_and_density

view = show_structure_and_density(fitted_model_file, density_map)
view