The program align output pdb file and extract pae plddt values to [.csv] for Alphafold 2.1.1

The programs was forked from plddt2csv (https://github.com/CYP152N1/plddt2csv)

Introduction movie was upload on Youtube.

https://youtu.be/sDsV7pr6T_A?t=358

$ cd /path/to/storage/

$ git clone https://github.com/CYP152N1/AF2align

This program was perfomend just by python3.

Modules (os, sys, pickle, csv, sys, time, numpy, argparse, math) were requred in python3 packeges.

$ cd /path/to/output/of/Alphafold2.1.1

$ python /path/to/storage/plddt2csv/align_mono.py

$ python /path/to/storage/plddt2csv/align_ptm.py

$ python /path/to/storage/plddt2csv/align_multi.py

If you align chain B at the three residues (20, 55, 80)

$ python /path/to/storage/plddt2csv/align_multi.py -alc 2 -al1 20 -al2 55 -al3 80

additional arguments were shown below.

'-i', default='result_model', help='input XXXXX if [XXXXX_Y_ptm.pkl]

'-m', default='relaxed_model', help='input ZZZZZ if [ZZZZZ_Y_ptm.pdb]

'-n', default='5', help='input Y if you want open [XXXXX_1_ptm.pkl,XXXXX_2_ptm.pkl ... ,XXXXX_5_ptm.pkl]

'-d', default='', help='ignored residue number for average pLDDTs caliculation to determined the ranking of models [1-5_56-75_105-135]; !!this argument is not suport for chain number!!.

'-alc', default="1", help='Change chain number from first chain to other chain

'-al1', default=0, help='Center the mid point of al1 and al3, the point (al1) shift on x-axis'; if -al1 = 0, 1/4 of residue number was used for alignment

'-al2', default=0, help='The point (al3) shift on xy-plane'; 3/4 of residue number was used for alignment'; 2/4 of residue number was used for alignment

'-al3', default=0, help='Center the mid point of al1 and al3, the point (al3) shift on x-asis and opozit site of al1'

??_plddt.csv

??pae_m????.csv