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patrickbryant1 / Umol

Protein-ligand structure prediction
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limit in protein length or msa sequence number? #5

Closed Yogesh1-11 closed 7 months ago

Yogesh1-11 commented 7 months ago

hi as a test case i was using a protein of 539 residue lenth and msa of 25 protein sequences. but i am getting memory exhaustion error. Is colab limited to protein length or msa size?

patrickbryant1 commented 7 months ago

Hi, the limit is on protein length. A statistical representation is created from the MSA and the size of this thereby doesn't matter. However, 25 sequences is probably too shallow to get good results.

Yogesh1-11 commented 7 months ago

even after chopping protein length to 490 error persists. what is the maximum protein length for umol? Also, I am using ion(

[O-]P(=O)([O-])[O-]) as ligand.

XlaRuntimeError Traceback (most recent call last)

in () 8 9 #Predict ---> 10 predict(config.CONFIG, 11 MSA_FEATS, 12 LIGAND_FEATS, ------------------------------ 9 frames ------------------------------ [... skipping hidden 14 frame] /usr/local/lib/python3.10/dist-packages/jax/_src/dispatch.py in backend_compile(backend, built_c, options, host_callbacks) 1010 # TODO(sharadmv): remove this fallback when all backends allow `compile` 1011 # to take in `host_callbacks` -> 1012 return backend.compile(built_c, compile_options=options) 1013 1014 # TODO(phawkins): update users. XlaRuntimeError: RESOURCE_EXHAUSTED: Out of memory while trying to allocate 8274444288 bytes. On Sun, Nov 19, 2023 at 2:24 PM Patrick Bryant ***@***.***> wrote: > Closed #5 as completed. > > — > Reply to this email directly, view it on GitHub > , or > unsubscribe > > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >
patrickbryant1 commented 7 months ago

This depends on the available RAM. Umol has no limit. I don't know what you have available in Colab, but recommend to run it locally for bigger proteins. We have not trained on phosphorylation sites.