Tom Goddard
Tom Goddard
Great! I will switch ChimeraX to using the new ColabFold when it is out of beta.
Atomic multi-state structures break some of the struct_group categories in the PDBx/mmCIF dictionary
The question is whether mmCIF atom_site allows multiple models which have different sets of atoms. I have never seen such a file. But I agree as long as every model...
There is a jax-metal backend created by Apple described here https://developer.apple.com/metal/jax/ I tried jax-metal version 0.0.4 with localcolabfold (https://github.com/YoshitakaMo/localcolabfold) on a MacBook Pro M1 Max (32 GPU cores, model MacBook18,2)...
As noted in my previous comment and Sergey's previous comment, jax-metal 0.0.4 is not working correctly on Apple ARM GPUs. If you are interested in trying it anyways, you simply...
Apple released new version 0.0.5 of jax-metal on December 21, 2023. I tried an alphafold run with localcolabfold on PDB 8ff2_A (40 amino acids) as in my comment above from...
[result_model_1_multimer_v2_pred_0.zip](https://github.com/deepmind/alphafold/files/10017395/result_model_1_multimer_v2_pred_0.zip)
Yes installing jax and jaxlib can work. But this effects thousands of users of ChimeraX and we don't want to ship jax and jaxlib with our application in order to...
The error traceback shows it is running energy minimization and that is where the error happened: File "/app/alphafold/alphafold/relax/amber_minimize.py", line 489, in run_pipeline ret.update(get_violation_metrics(prot)) You probably need --run-relax=false to not use...
Maybe the way to specify this option is "--norun_relax".
While the solution in the June 17, 2022 comment of replacing the the !zip shell magic with an os.system() call will work on the first ColabFold prediction, if you run...