lzhangUT

runtime Error:

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Hi, I am having issue running the last step of AlphaFold.ipynd on the Colab. The error I am having is: /usr/local/lib/python3.7/dist-packages/jax/_src/tree_util.py:189: FutureWarning: jax.tree_util.tree_multimap() is deprecated. Please use jax.tree_util.tree_map() instead as...

how to specify db-load-mode in precomputed_alignments_mmseqs.py

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Hi, I am using the recomputed_alignments_mmseqs.py to search for MSA for my input.fasta which has 9 sequences inside. but the mmseq2 is taking too long to run it, it is...

cpu not fully used

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Hi, I am running precomputed_alginment_mmseqs.py, everything is up running (for now). but when I check the usage of cpus (my Vitural machine has 6 vcpus), it seems like mmseqs is...

how to use .a3m file as input

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Hi, Can i use fastfold to run just inference? for example, I dont need jackmmer to run the msa search, I already have my msa search result (.a3m file) ready....

Couldn't use amber in colabfold_batch, after running colabfold_search

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Hi, I have followed all the steps on your GitHub using pip install (not localcolabfold), and everything worked fine. I downloaded all the data to my machine, and was able...

colabfold_search and colabfold_batch takes too long than expected

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Hi there, Thanks for sharing colabfold. It is greatly appreciated. we followed the exact step on the github using 'Running locally'. we have a virtual machine with 6cCPUs, 112 RAM,...

Hi, Really appreciate your work, it is very helpful to what I am working on right now. I am kinda newbie in deep learning of protein sequences, forgive me if...

## Expected Behavior a fasta file with ID and sequences ## Current Behavior ## Steps to Reproduce (for bugs) mmseqs databases UniProtKB db/uniprot tmp mmseqs createdb input_fasta queryDB mmseqs search...

Hi Thanks for the great contributions here. I have a fasta file containing 36 sequences, I am trying to do the homology search against uniprot, Here is what I did:...

wild type sequence for stability dataset

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Hi, I am interested in using you tape data for my deep learning, but we would like to generate pdb file from the wild type sequence first. we sort of...