Jue Wang

Not sure what's going on here, but the inpainting method in this repository is actually quite old at this point. RFDiffusion was just released today -- it is much better....

Can you send the command you ran, and maybe the input pdb? On Thu, Aug 11, 2022 at 12:02 PM philhuett ***@***.***> wrote: > I have successfully hallucinated various proteins,...

Sorry, not sure why this isn't in the environment yaml. Easiest is probably just to install it yourself: pip install dm-tree On Mon, Aug 22, 2022 at 4:56 AM Jakob...

Sorry, I thought I added it after aravinda1879's message but I guess it slipped my mind. It should be there now.

This output is expected. These inpainting checkpoints aren't good at building regions longer than ~20 residues. If you, for instance, use --window A,2,8 (rebuild that region only), you'll get more...

Sorry we didn't explain this more clearly in the README. We provided alphafold code but not weights, so you need to install those yourself. I think the best option is...

This script is actually obsolete. We used to use a bunch of different scoring metrics, but more recently we have mostly focused on AF2 predictions. This doesn't require as much...

Yes, you're right, there is a typo in the comment. It seems there is an equals sign where a minus/hyphen should be. On Tue, Dec 6, 2022 at 11:24 AM...

I don't quite remember if we've seen this. If you send me example inputs and outputs I might be able to look into it further. Also, just a tip --...

we've made major changes to the inpainting script with a recent update. give the new version a try (there is no longer a window mode, only contig) and see if...