consurf.md

Consurf

Migrate Consurf scores from the file consurf.grades to a Pyrosetta pose.

from typing import *

def add_bfactor_from_consurf(pose: pyrosetta.Pose, grades_filename:str, strict:bool=True):
    """
    Adds the bfactors from a consurf run to a pose based on the PDB residues.
    ``replace_res_remap_bfactors`` or ``set_bfactors_from_atom_id_map``
    were not used but may have been a cleaner strategy. This was quicker to write.

    The Consurf download folder, something like ``Consurf_Outputs_123456789``,
    contains a file ``consurf.grades``: this path is the ``grades_filename`` argument.
    
    when ``strict`` is true an error is raised in the residues do not match.
    """
    conscores = read_conscores(grades_filename)
    add_bfactors_from_conscores(pose, conscores, strict)
    return conscores

def read_conscores(grades_filename: str) -> dict:
    conscores = {} # key is MET1:A
    with open(grades_filename) as r:
        for row in r:
            row = row.strip()
            if not len(row) or not row[0].isdigit():
                continue
            parts = row.split()
            conscores[parts[2]] = float(parts[3])
    return conscores
    
def add_bfactors_from_conscores(pose: pyrosetta.Pose, conscores:dict, strict:bool=True):
    """
    Adds the conscores dictionary to bfactor in place.
    """
    pdb_info = pose.pdb_info()
    pdb2pose = pdb_info.pdb2pose
    for con_res in conscores:
        pose_res = pdb2pose(res=int(con_res[3:-2]), chain=con_res[-1])
        if pose_res == 0:
            continue
        residue = pose.residue(pose_res)
        if strict:
            assert residue.name3() == con_res[:3], f'{residue.name3()} ≠ {con_res[:3]}' 
        for i in range(residue.natoms()):
            pdb_info.bfactor(pose_res,i, conscores[con_res])
        
def remap_conscores_chains(conscores:dict, chain_map: Dict[str, str]) -> dict:
    """
    Say conscores is chain A based, but the model is not.
    """
    return {res[:-2]+':'+chain_map[res[-1]]: score for res, score in conscores.items()}

Basic example:

add_bfactor_from_consurf(med27, 'Consurf_Outputs_1606141517/consurf.grades')

Chain is A in consurf but V in pose example:

conscores = read_conscores('Consurf_Outputs_1606141517/consurf.grades')
remap_conscores_chains(conscores, {'A': 'V'})
add_bfactors_from_conscores(pose, conscores)

PyMOL

b-factor putty preset is in rainbow. This is a better option:

cartoon putty
spectrum b, blue_white_red
color atomic, not element C

Alternatively, if not for publication green to red may be better: green_white_red.

To disable putty:

cartoon automatic
color atomic