Sergey O
Sergey O
Thanks for the report! I've pushed an update that will print ipae and iptm when more than a single chain is present, regardless if it satisfies the "binder" protocol condition...
One more thing to keep note, if you specify multiple chains, they will be FROZEN with respect to each other. if you want to fix or control part of the...
By frozen, what I mean is the chains you specify wont "dock" to come into contact, they will remain relatively at the same distance/orientation as you provide in the input....
Sorry, looks like my fix earlier didn't work. I'll try fix this later today. Reverting back for now.
Edits I had to make: https://github.com/sokrypton/esm3/commit/f8a9f0dca35cd731f488c7830aa5c155fa91d14b
ColabDesign integrates lots of different protocols. The alphafold interface that bindcraft uses is licensed as BEERWARE: https://github.com/sokrypton/ColabDesign/blob/main/af/LICENSE.txt
I've updated license to include the entire repo. So should be fine!
Thanks! I've fixed this in v1.1.1 branch.
When only a single sequence is provided, alphafold is limited to what it can predict. If you have reason to believe that the region you are constraining will fold regardless...
I added a patch that should hopefully fix this. Can you try again: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb