how to run pTM flavour of AlphaFold2? (i.e to get PAE and TM)

kalininalab / alphafold_non_docker

AlphaFold2 non-docker setup

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how to run pTM flavour of AlphaFold2? (i.e to get PAE and TM) #21

Closed DLMURPHY150 closed 1 year ago

DLMURPHY150 commented 2 years ago

Hi guys,

This is not per se' an issue but I've just used your framework to run non-docker AlphaFold2 with "full_dbs" preset for which I was expected in the output per-model .pkl files the PAE matrix and predicted TM-score which I did not get. My understanding was that running "full_dbs" preset runs the ptm network instead of casp14?!

Can anyone check this or confirm how to run the ptm version in AlphaFold2 with your main python script please?!

Thanks, David

sanjaysrikakulam commented 2 years ago

Hi @DLMURPHY150

Apologies for the delayed response. I have updated the non-docker version to support everything that AF2 docker does. Using the latest version now should enable pTM flavour as well (use -m monomer_ptm -c full_dbs).