yamabuki-chan
yamabuki-chan
hmmsearch and hhsearch are used for template search. Therefore it will run even if --use_precomputed_msas flag is present. https://github.com/google-deepmind/alphafold/issues/469#issuecomment-1131870718 The DBs for templates are relatively small so it would not...
I think there is no way to redirect without changing some lines of the python script. I think the easiest way to speed up is increase the number of cpus...
Template search (hmmsearch, hhsearch) is not controlled by --use_precomputed_msas flag, I think. https://github.com/google-deepmind/alphafold/blob/632ef575c64eff9eb5ed96c8c7b055bf675421ac/alphafold/data/pipeline.py#L184-L191
You are running hhblits instead of AlphaFold. hhblits considers the -i file to be an "MSA" and therefore complains that the MSA provided is invalid. The solution depends on what...
I think issues about ColabFold can be discussed in https://twitter.com/sokrypton/status/1553733908189028353 If my understanding of the conversation on the server is correct, (I am not using ColabFold so much) ・The issue...
> I used the same software online and tried to run a "pip install biopython==1.81" on VSCode terminal on my computer, but nothing changed. Is your VSCode terminal attached to...
`--model_names=monomer` may be `--model_preset=monomer`.
> Using your suggested parameter gives a different error about using a wrong parameter. The parameters in my command are correct. How about `--model_names=model_1` then?
> 11:42:53.447 WARNING: Ignoring invalid symbol '*' at pos. 1623 in line 2 of /tmp/tmpd42j2lo8/query.a3m Don't you have '\*' at the end of the query sequence?
https://github.com/deepmind/alphafold/blob/c128d1aa2c21407fbe51d3cd87b85d4c5942056d/alphafold/data/pipeline_multimer.py#L144 ~Changing this line may be better.~ (Edit: Changing codes in early steps introduces bugs easily & other ids also start from 1, thus it may be not so good....