plddt2csv

Extract the PAE & pLDDT value of Alphafold ver. 2.0.0 from .pkl to .csv & .pdb file.

Alinment program of .pdb files were updated for Alphafold ver. 2.1.1

(align_mono.py, align_ptm.py, align_multi.py)

https://github.com/CYP152N1/AF2align

---

Introduction movie was upload on Youtube.

Japanese var. (plddt_align.py)

https://youtu.be/qiw5DbzZcUE

for Alphafold 2.1.1 (align_mono.py, align_ptm.py, align_multi.py)

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

Update information

"align_multi.py", "align_mono.py" and "align_ptm.py" were released.

This version was created for alphafold 2.1.1. to align .pdb files

This script can be parformed without any argument.

$ cd /path/to/output/directory

$ python align_mono.py

It is omitted that the inthersion of pLDDT at b-factor on ".pdb format", because pLDDT was already writtened in out put file of AF 2.1.

additional argument can be observed by

$ python align_mono.py -h

multimer version can be select alinment chain by

$ python align_multi.py -alc 2

The default value of -arc argument is 1 for the alignment of A chain.

These alignment program will be separated to another programs, because program content and name don't match.

---

"pae2csv.py", "pae2png.py", "plddt_align_ptm.py", and "ptm_docker.py" were released

[pae2csv.py] generates [p2c_pae_?.csv] & [p2x_plddt.csv].

[p2c_pae_?.csv] contains Predicted Aligned Error (PAE).

You can visualize using Excel like the figure shown below.

Thanks Dr. Yoshitaka Moriwaki (@Ag_smith) for showing how to export predicted aligned error in alphafold2.

To extract "PAE" into [result_model_?.pkl], we need to change [docker/run_docker.py]

[ptm_docker.py] creates run_docker_ptm.py from your run_docker.py.

model_names of [run_docker_ptm.py] was changed to "model_?ptm" from "model?"

$ cd /path/to/storage/

$ git clone https://github.com/CYP152N1/plddt2csv

$ cd /path/to/Alphafold2

$ python3 /path/to/Alphafold2/ptm_docker.py

$ python3 docker/run_docker_ptm.py --fasta_paths=/path/to/.fasta --max_template_date=2020-05-14

If you performe "run_docker_ptm.py" instead of "run_docker.py",

result_model_?_ptm.pkl posesses predicted_aligned_error value.

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

$ python3 /path/to/storage/plddt2csv/pae2csv.py

           or

$ python3 /path/to/storage/plddt2csv/plddt_align_ptm.py

If you perform "run_docker_ptm.py" instead of "run_docker.py"_ptm,

you cannot use plddt_align.py and plddt2csv.py

[pae2png.py] generates [p2c_pae_?.png] using matplotlib & seaborn.

You need to perform below comands.

$ pip3 install matplotlib

$ pip3 install seaborn

---

-m arguments was introduced in plddt_align.py & plddt_align_ptm.py.

If you don't perform amber_minimization,

or amber_minimization was clashed on first model

python3 plddt_align.py -m unrelaxed_model

           or

python3 plddt_align.py -m unrelaxed_model -n 1

---

plddt_align.py was released

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

$ python3 /path/to/storage/plddt2csv/plddt_align.py

This program automatically generates [align_xxxx_?.pdb]s.

These .pdb files will be aligned each other.

These .pdb including pLDDT instead of b-factor.

---

-d arguments was introduced.

python3 plddt2csv.py -d 1-30_53-

           or

python3 plddt_align.py -d 1-30_53-

avarage pLDDT will be caliculate without residue number from 1 to 30 and from 53 to C-terminus.

["current folder name"_?_pLDDT??.pdb] will be also generated. default value is ""

---

How to Use

$ cd /path/to/storage/

$ git clone https://github.com/CYP152N1/plddt2csv

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

$ python3 /path/to/storage/plddt2csv/plddt2csv.py

                     or

$ python3 /path/to/storage/plddt2csv/plddt_align.py

---

This program generates [plddt.csv] and [relaxed_"current folder name"?.pdb] or [align"current folder name"_?.pdb]

form [features.pkl], [result_model_?.pkl] and [relaxed_model_?.pdb]

plddt.csv show plddt value of each residue of all relaxed models.

output pdb file contain plddt value in B factor region. High plddt value means high condidence of the output structure. You can check plddt put the colored by b-factor on the structure using model viewer such as pymol.

arguments can be chack by $ Python3 /path/to/storage/plddt2csv.py -h