grandrea / alphacrop

split AlphaFold 2.x and 3.x models by confidence

AlphaCrop

split AlphaFold 2.x and 3.x models by confidence. Works on both pdb and cif files. Needs biopython bio.pdb module.

Run with

python alphacrop.py --filename mystructure.pdb

or mystructure.cif. If needed, explicitly specify file format with the --file_format flag

Confidence defined by Deepmind, each input into multiple files made up of:

• only very high confidence regions (plDDT > 90)
• only confident regions and above (plDDT > 70)
• only low concfidence regions and above, discarding very low confidence (plDDT > 50)

Essentially splits the file by b-factor column, generating 3 files.

Also available as colab here https://colab.research.google.com/drive/1kfF_Kkozi5ox8mVebqKgvc7UEWdXWpnf?usp=sharing