openfold

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Training Runtime Error: StopIteration

36

Hi, I'm using the released training data on AWS and the latest main branch to train the model. 1. The directory structure of the released data is not recognized by...

bozhang-hpc

cpu not fully used

2

Hi, I am running precomputed_alginment_mmseqs.py, everything is up running (for now). but when I check the usage of cpus (my Vitural machine has 6 vcpus), it seems like mmseqs is...

lzhangUT

Unusual predicted structures from pretrained OpenFold on Pascal GPU

10

This is most likely some kind of local configuration error, but I haven't been able to pin down the cause. If anyone has encountered this behavior before or has an...

epenning

Does Training support Chunking?

7

Hello, I look forward to observing the dynamics of the network during training. I noticed that Chunking is turned off during training, and there is related assert in code, so...

gofreelee

Feature request: retain model ensembling as an option, for molecular replacement usage purposes

8

Hello, Although it is true that in most cases the 5/25 models generated by AF2 monomer/multimer are very similar to each other, we consistently find that - when using these...

lucajovine

Is this model a dynamic model?

1

By dynamic model, I mean if the computation logic can be decided by the input. Is there any conditional computation in openfold? Thanks in advance.

luckyq

mmseqs inference

3

There is clear instructions on running Alphafold on its original sequence alignment protocol but that on mmseqs is unclear. Is mmseqs supported for both monomeric and multimeric structures? If so,...

kchu02

Failing to run the inference script

3

## No such file or directory: 'fasta_dir' I have created my conda environment and downloaded all the data required in the readme file. However, I couldn't run the inference file...

liuyixin-louis

Hey @gahdritz Awesome milestone with v1.0! This is super exciting for the community. I wondered if you would be interested to take this even further by creating a Lightning App....

tchaton

RuntimeError: Error compiling objects for extension

3

I installed the env by the script and when I ran the setup.py, an error occurred. RuntimeError: Error compiling objects for extension

zjyuan1208