Usage

To use PDB Manip Python in a project:

from pdb_manip_py import pdb_manip
pdb_manip.show_log()

Create a Coor() object

You can either get the coordinates from the Protein Data Bank:

coor_1hsg = pdb_manip.Coor()
coor_1hsg.get_PDB('1hsg')

Succeed to read file 1hsg.pdb ,  1686 atoms found

Or load a local stored file:

coor_1hsg = pdb_manip.Coor('./1hsg.pdb')

Succeed to read file 1hsg.pdb ,  1686 atoms found

Extract selection of coordinates

You can extract a selection of coordinates, here we will use the 1hsg.pdb PDB file and extract the coordinates of L-735,524 an inhibitor of the HIV proteases (resname MK1):

# Select res_name MK1
lig_coor = coor_1hsg.select_part_dict(selec_dict={'res_name': ['MK1']})

The obtain selection can be saved using the write_pdb() function:

# Save the ligand coordinates
lig_coor.write_pdb('1hsg_lig.pdb')

Succeed to save file 1hsg_lig.pdb

For selection you can use :

• name for atom name

• alter_loc alternative location

• res_name residue name

• chain chain ID

• res_num residue number

• uniq_resid a unique residue number starting from 0

• insert_res insert residue

• xyz x, y, z, coordinates

• occ occupation

• beta beta factor

Selector can be combined, eg. to select residue names Proline and Alanine from chain A you can use:

PRO_ALA_A_coor = coor_1hsg.select_part_dict(
    selec_dict={'res_name': ['PRO', 'ALA'], 'chain': ['A']})

note:

To select protein atoms you can use the PROTEIN_AA variable containing protein residue name, giving this selector:

selec_dict={'res_name': pdb_manip.PROTEIN_AA)}

Visualize coordinates in pseudo 3D

• using matplotlib

• Inspired from sokrypton in https://github.com/sokrypton/ColabFold

_ = coor_1hsg.plot_pseudo_3D('beta')

Visualize coordinates in 3D

You can use the nglview library to vizualise in 3D your protein.

view = coor_1hsg.view
view

IFrame(src='../_static/1hsg.html', width=600, height=300)