deepmind/alphafold issues and pull requests

#713 - v2.3.1 generates errors for multimer

Issue - State: open - Opened by nmrworker almost 2 years ago - 3 comments

#712 - Docker build test

Pull Request - State: closed - Opened by jkwmoore almost 2 years ago - 1 comment

#711 - Colab Notebook - OpenMMException: Particle coordinate is nan

Issue - State: closed - Opened by biobrett6 almost 2 years ago - 3 comments

#710 - Does CUDA version matter?

Issue - State: open - Opened by johnny-rodriguez almost 2 years ago - 3 comments
Labels: setup

#709 - Multimer colab erroring out in JAX with 'incompatable shapes for broadcasting ...'

Issue - State: open - Opened by sroet almost 2 years ago

#708 - 'uniref30_database_path

Issue - State: open - Opened by satya1102 almost 2 years ago - 5 comments
Labels: setup

#707 - module 'lib' has no attribute 'OpenSSL_add_all_algorithms'

Issue - State: closed - Opened by bioaurbehno almost 2 years ago - 4 comments

#706 - Error in installation ...

Issue - State: open - Opened by premlatamajhi almost 2 years ago - 3 comments

#705 - Is this a memory error?

Issue - State: open - Opened by Sparklibug almost 2 years ago - 1 comment

#704 - Alphafold Version

Issue - State: closed - Opened by stefanoliver almost 2 years ago - 1 comment
Labels: usage question

#703 - afdb - retrieving accession_ids.csv and sequences.fasta

Issue - State: closed - Opened by joegeorgeson almost 2 years ago - 10 comments

#702 - Unable to build

Issue - State: closed - Opened by methylome almost 2 years ago - 5 comments
Labels: setup

#701 - Alphafold v2.3 multimer structure is worse than v2.2 multimer

Issue - State: open - Opened by johnny-rodriguez almost 2 years ago - 1 comment

#700 - Updated cuda base image.

Pull Request - State: open - Opened by enthus1ast almost 2 years ago - 2 comments

#699 - No CUDA device is available - Alphafold2 Multimer Folding Issue

Issue - State: open - Opened by akenginorhun almost 2 years ago - 1 comment

#698 - Clarify explanation of `ranked_*.pdb` output in README

Pull Request - State: open - Opened by ulupo almost 2 years ago - 3 comments

#697 - pdb_seqres.txt,length is empty

Issue - State: closed - Opened by wh277 almost 2 years ago

#696 - Enabling Unified Memory on Compute Cluster

Issue - State: open - Opened by DrJesseHansen almost 2 years ago - 3 comments
Labels: out of memory

#695 - How to only extract MSA use AlphaFold multimer？

Issue - State: open - Opened by alanfengjiang almost 2 years ago - 2 comments
Labels: usage question

#694 - TypeError: Dtype object is not a valid JAX array type.

Issue - State: open - Opened by Joshsamuel101 almost 2 years ago - 4 comments
Labels: setup

#693 - AlphaFold-multimer v3 training data

Issue - State: closed - Opened by gezmi almost 2 years ago - 1 comment

#692 - Error compiling program: nvrtc: error: invalid value for --gpu-architecture (-arch)

Issue - State: closed - Opened by MarkusRainerSchmidt about 2 years ago - 5 comments
Labels: setup, relax

#682 - ValueError: Could not find hmmsearch database

Issue - State: closed - Opened by katarinazosel about 2 years ago - 6 comments
Labels: setup

#678 - confusing result after running alphafold-multimer

Issue - State: closed - Opened by lamyankin about 2 years ago - 2 comments
Labels: usage question

#676 - Use precomputed pdb_hits.sto

Issue - State: open - Opened by davidyanglee about 2 years ago - 4 comments
Labels: usage question

#671 - uniref90 can't download

Issue - State: closed - Opened by hezhiqiang8909 about 2 years ago - 10 comments
Labels: setup

#666 - Colab pro + failing to predict >2000 residues

Issue - State: closed - Opened by HBCH1 about 2 years ago - 7 comments
Labels: colab, out of memory

#665 - Memory issue when processing large protein. Is my swap not being leveraged

Issue - State: open - Opened by cheminformaticist about 2 years ago - 5 comments
Labels: out of memory

#656 - uniref30_database_path issue

Issue - State: closed - Opened by limh25 about 2 years ago - 5 comments

#636 - Running without MSA features

Issue - State: open - Opened by Gabriel-Ducrocq about 2 years ago - 7 comments
Labels: usage question

#592 - one error about alphafold，ask for help online

Issue - State: open - Opened by 285880830 over 2 years ago - 2 comments

#573 - DeepMind AlphaFold2 colab notebook already crashes during 3rd party software installation cell

Issue - State: closed - Opened by MWNautilus over 2 years ago - 6 comments
Labels: error report, docker

#569 - hmmsearch failed: Parse failed (sequence file /path/pdb_seqres/pdb_seqres.txt): Line 1360234: illegal character 0

Issue - State: closed - Opened by jsnelsonbsu over 2 years ago - 7 comments
Labels: duplicate, third-party tool

#542 - ETL (msa+templates) should be separated from inference

Issue - State: open - Opened by andreadisimone over 2 years ago - 2 comments
Labels: feature request

#541 - hhalignment.cpp:3539: MergeMasterSlave error

Issue - State: closed - Opened by derf0 over 2 years ago - 3 comments
Labels: third-party tool

#533 - Installing 3rd party software on Colab not working

Issue - State: closed - Opened by quockerwodger over 2 years ago - 2 comments
Labels: colab

#531 - Does alphafold support proteins with non-canonical aminoacids such as selenocysteine?

Issue - State: open - Opened by abhinavb22 over 2 years ago - 4 comments
Labels: usage question

#498 - Unable to initialize backend 'gpu'

Issue - State: open - Opened by caom92 over 2 years ago - 7 comments

#475 - ValueError: Could not find Jackhmmer database /mnt/uniprot_database_path/uniprot.fasta

Issue - State: open - Opened by Pharmacy-student over 2 years ago - 8 comments
Labels: setup

#437 - Faster MSA computations with chunked DBs on Colab

Issue - State: open - Opened by Meghpal almost 3 years ago - 1 comment

#434 - How to align chain ID of two complexes before running DockQ?

Issue - State: open - Opened by nonononanana almost 3 years ago - 2 comments

#427 - Use of use_precomputed_msas

Issue - State: open - Opened by calmip almost 3 years ago - 4 comments

#425 - Job was killed with `/app/run_alphafold.sh: line 3: 8 Killed python /app/alphafold/run_alphafold.py "$@"``

Issue - State: open - Opened by songyinys almost 3 years ago - 4 comments

#403 - On docker after some time: No compatible CUDA device is available

Issue - State: open - Opened by Wolf-Z almost 3 years ago - 8 comments
Labels: docker, cuda

#399 - Parallel execution of MSA tools

Pull Request - State: open - Opened by fuji8 almost 3 years ago - 13 comments

#392 - 'Out of memory' error

Issue - State: closed - Opened by wentski almost 3 years ago - 8 comments
Labels: error report, out of memory

#383 - Error in Alpha Fold multimer

Issue - State: closed - Opened by galshuler almost 3 years ago - 11 comments
Labels: relax

#339 - AF2 non-docker in a cluster enviroment

Issue - State: closed - Opened by JuergenUniVie about 3 years ago - 6 comments
Labels: duplicate, usage question, setup

#331 - run_docker.py SyntaxError: invalid syntax in line 83

Issue - State: closed - Opened by haoecust about 3 years ago - 1 comment

#327 - Trouble downloading pdb_mmcif database

Issue - State: closed - Opened by NMMQ about 3 years ago - 3 comments
Labels: third-party tool, setup

#321 - Updated Dockerfile to address incompatibilities during setup

Issue - State: closed - Opened by mbassalbioinformatics about 3 years ago - 2 comments
Labels: error report, duplicate

#280 - RuntimeError: Jackhmmer failed

Issue - State: closed - Opened by kdpan about 3 years ago - 2 comments

#252 - mmCIF output

Issue - State: open - Opened by brindakv about 3 years ago - 12 comments
Labels: feature request

#251 - Improper chain IDs when running Multimer model

Issue - State: open - Opened by nzrandol about 3 years ago - 3 comments
Labels: error report

#197 - RuntimeError: Resource exhausted: Out of memory while trying to allocate 12582912 bytes.

Issue - State: closed - Opened by Ozcifci over 3 years ago - 10 comments
Labels: out of memory

#164 - HHblits failed problem

Issue - State: closed - Opened by Davidswang over 3 years ago - 3 comments

#143 - Singularity Definition

Issue - State: closed - Opened by jdhayes over 3 years ago - 6 comments
Labels: feature request, setup

#135 - Alphafold exits without result, but with warning of maximum number of residues 32763 exceeded in sequence

Issue - State: closed - Opened by qingsongli1979 over 3 years ago - 7 comments
Labels: error report, third-party tool

#122 - ptxas returned an error during compilation of ptx to sass

Issue - State: closed - Opened by 2subzero over 3 years ago - 8 comments
Labels: error report

#107 - docker.errors.ImageNotFound: 404 Client Error when running python3 docker/run_docker.py

Issue - State: closed - Opened by rainwala over 3 years ago - 9 comments

#97 - RuntimeError: HHblits failed

Issue - State: closed - Opened by huangjk1103 over 3 years ago - 18 comments
Labels: error report

#24 - Non docker setup

Issue - State: closed - Opened by sanjaysrikakulam over 3 years ago - 15 comments
Labels: setup

GitHub / deepmind/alphafold issues and pull requests