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Hi AF2 team!
I'm chiming in to see if you all might be open to modifying some of the Python wrappers to external tools such that they automatically use all CPUs available?
I did a quick audit of…
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hi, i ran into a similar issue as https://github.com/soedinglab/hh-suite/issues/337 and https://github.com/google-deepmind/alphafold/issues/661. i have also tried -db_preset (as suggested in #661) but…
deskk updated
12 months ago
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Hi - thanks for the great library. I'm interested to know whether there is a way to do the mmseqs (bucket-based 'diversity-aware') filtering that is used by default in ColabFold on a set of a3m files …
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Great work !
I've successfully predict protein-SM complex structure using demo_6zcy.json, just similar with given predicted structure in demo_output. However, use of demo_6zcy_smiles.json failed. Ple…
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Last day, I make some experiments in a Server to run the
`./run_alphafold.sh -d /dataset/ -o result -p monomer -m model_2 -i input/T1061.fasta`
and I read the log, confused, the T1061 is 949AA.
`…
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Here is the paper:
4.2.1 CPU acceleration. To accelerate the CPU stage, three independent sequential MSA searches can be arranged in parallel (Fig 4). Due to the limited CPU cores accompanying GPUs…
wttat updated
2 years ago
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I tried to search a fasta file containing ids more than 31 characters using hhblits, which resulted in an opaque error message when hhblits reached that sequence.
## Expected Behavior
hhblits wo…
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Hi all
I meet a problem that
E0226 17:51:54.905934 139873214023488 hhsearch.py:56] Could not find HHsearch database ./alphafold_data//pdb70/pdb70
Traceback (most recent call last):
File "/home…
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I'm getting an error on the hhsearch step:
`Running hhsearch
./run_pipeline.sh: line 49: 7701 Segmentation fault (core dumped) $HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr -v 0 > $WDIR…
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I run
./run_e2e_ver.sh example/input.fa example/t1
the result:
# ll example/t1/
drwxr-xr-x 4 root root 4096 8月 10 17:54 ./
drwxr-xr-x 8 root root 4096 8月 10 16:36 ../
drwxr-xr-x 2 root…