Comments (3)
bjing2016
commented on August 19, 2024
Can you check if the OpenFold version is correct? A previous version of the README had the wrong install command --- see #2 where the issue sounds similar to what you describe with the ExtraMSAStack.
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jfreeze95
commented on August 19, 2024
Yep, that was it. Thanks!
In case anyone asks, the git request for the commit from OpenFold you specify won't work if you have Cuda 12.3, which is what led me to try the latest OpenFold commit which did work with 12.3 before I got Cuda 11.6 setup.
Also, in mmseqs_query line 284 you have a hard-coded iloc[:3] which only allows the first three entries of a csv file to be processed. I ran into that when trying to use the atlas_test.csv file which will then throw an error during inference when it can't find the 4th entry's mmSeq folder.
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bjing2016
commented on August 19, 2024
Thanks, mmseqs_query has been fixed.
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Related Issues (20)
- TypeError: __init__() missing 1 required positional argument: 'no_column_attention' HOT 5
- Multimer HOT 2
- scripts.unpack_mmcif.py reference to outdated betafold? HOT 1
- Installation fails on Cuda12 HOT 3
- PDB as input
- PPI ensembles HOT 2
- Dockerfile or CUDA 12 HOT 2
- Diffuse selected residues
- Issues with CUDA12 and or G++17 HOT 1
- Command options' help messages in predict.py missing HOT 1
- Appropriate `model_config` arguments for initial training upon predicting with long sequence HOT 2
- Generating Abnormal PDB results HOT 2
- missing scripts.prep_atlas.py file HOT 1
- The size of tensor a (184) must match the size of tensor b (183) at non-singleton dimension 1 HOT 1
- Availability of MD Ensemble Evaluation Scripts HOT 2
- Training with PDBs
- The distance between adjacent alpha carbons is not 3.8 A from the Prior
- when traing alphaflow from scratch, show AttributeError: 'AlphaFoldWrapper' object has no attribute 'extra_msa_stack' HOT 2
- predict.py does not run AttributeError: module 'numpy' has no attribute 'object'.
- Diffusion scheduling code making abnormal protein output
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