openfold

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I have a situation where I have one wild-type sequence and a few thousand variants of that wild-type sequence that I've built with a generative model. To speed up inference,...

brucejwittmann

Both Docker and conda installation failing

3

Hello! I have attempted to install openfold via both docker and the install script (I already have an existing conda install I don't want nuked, so I selectively ran the...

n-garc

Hello! I've been using Openfold for a while, mostly for inference, but I would like to try training it for a specific type of fold. From your paper I understand...

Teohoho

Multi-chain support?

2

Hi, first of all: absolutely great work - thank you so much for putting so much time and effort into sharing the training code for SOTA structure prediction! :) From...

mheinzinger

openfold.utils.kernel.csrc' as an importable package[^1], when pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'

2

Hello I try to install diffdock on a linux station(redhat 7.3) (from https://github.com/gcorso/DiffDock) When i did the last step : pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307' I had a fatal error...

Alain-chavanieu

ValueError: Could not find HHBlits database path/uniclust30_2018_08

6

Hey guys Great work! I am trying to get OpenFold running on our cluster and having problems with hhblits on uniclust30. I adapted the longer paths to just "path" for...

ArsLeicholt

Hello everyone! I want to try train openfold model on small amount of data for understanding the process. How can I generate alignment_dir? Or where can I find ready data?...

vetmax7

* This PR fixes typos and clarifies wording in the docstrings of `residue_constants.py`.

amorehead

RuntimeError: attn_softmax_inplace_forward_ not implemented on CPU

4

What's this error? Is there any prepared jod when I try to run? 'RuntimeError: attn_softmax_inplace_forward_ not implemented on CPU'

JeongSooNa

Openfold not compatible with newest Flash attention 2.0.4

2

Hi, I upgraded to flash attention 2.0.4, which breaks imports in the OpenFold package. Will there be an upgrade to make OpenFold compatible? Thanks Here the traceback: `Traceback (most recent...

OliviaViessmann