Ecosyste.ms: Issues
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GitHub / deepmind/alphafold issues and pull requests
#713 - v2.3.1 generates errors for multimer
Issue -
State: open - Opened by nmrworker over 1 year ago
- 3 comments
#712 - Docker build test
Pull Request -
State: closed - Opened by jkwmoore over 1 year ago
- 1 comment
#711 - Colab Notebook - OpenMMException: Particle coordinate is nan
Issue -
State: closed - Opened by biobrett6 over 1 year ago
- 3 comments
#710 - Does CUDA version matter?
Issue -
State: open - Opened by johnny-rodriguez over 1 year ago
- 3 comments
Labels: setup
#709 - Multimer colab erroring out in JAX with 'incompatable shapes for broadcasting ...'
Issue -
State: open - Opened by sroet over 1 year ago
#708 - 'uniref30_database_path
Issue -
State: open - Opened by satya1102 over 1 year ago
- 5 comments
Labels: setup
#707 - module 'lib' has no attribute 'OpenSSL_add_all_algorithms'
Issue -
State: closed - Opened by bioaurbehno over 1 year ago
- 4 comments
#706 - Error in installation ...
Issue -
State: open - Opened by premlatamajhi over 1 year ago
- 3 comments
#705 - Is this a memory error?
Issue -
State: open - Opened by Sparklibug over 1 year ago
- 1 comment
#704 - Alphafold Version
Issue -
State: closed - Opened by stefanoliver over 1 year ago
- 1 comment
Labels: usage question
#703 - afdb - retrieving accession_ids.csv and sequences.fasta
Issue -
State: closed - Opened by joegeorgeson over 1 year ago
- 10 comments
#702 - Unable to build
Issue -
State: closed - Opened by methylome over 1 year ago
- 5 comments
Labels: setup
#701 - Alphafold v2.3 multimer structure is worse than v2.2 multimer
Issue -
State: open - Opened by johnny-rodriguez over 1 year ago
- 1 comment
#700 - Updated cuda base image.
Pull Request -
State: open - Opened by enthus1ast over 1 year ago
- 2 comments
#699 - No CUDA device is available - Alphafold2 Multimer Folding Issue
Issue -
State: open - Opened by akenginorhun over 1 year ago
- 1 comment
#698 - Clarify explanation of `ranked_*.pdb` output in README
Pull Request -
State: open - Opened by ulupo over 1 year ago
- 3 comments
#697 - pdb_seqres.txt,length is empty
Issue -
State: closed - Opened by wh277 over 1 year ago
#696 - Enabling Unified Memory on Compute Cluster
Issue -
State: open - Opened by DrJesseHansen over 1 year ago
- 3 comments
Labels: out of memory
#695 - How to only extract MSA use AlphaFold multimer?
Issue -
State: open - Opened by alanfengjiang over 1 year ago
- 2 comments
Labels: usage question
#694 - TypeError: Dtype object is not a valid JAX array type.
Issue -
State: open - Opened by Joshsamuel101 over 1 year ago
- 4 comments
Labels: setup
#693 - AlphaFold-multimer v3 training data
Issue -
State: closed - Opened by gezmi over 1 year ago
- 1 comment
#692 - Error compiling program: nvrtc: error: invalid value for --gpu-architecture (-arch)
Issue -
State: closed - Opened by MarkusRainerSchmidt over 1 year ago
- 5 comments
Labels: setup, relax
#682 - ValueError: Could not find hmmsearch database
Issue -
State: closed - Opened by katarinazosel over 1 year ago
- 6 comments
Labels: setup
#678 - confusing result after running alphafold-multimer
Issue -
State: closed - Opened by lamyankin over 1 year ago
- 2 comments
Labels: usage question
#676 - Use precomputed pdb_hits.sto
Issue -
State: open - Opened by davidyanglee over 1 year ago
- 4 comments
Labels: usage question
#671 - uniref90 can't download
Issue -
State: closed - Opened by hezhiqiang8909 over 1 year ago
- 10 comments
Labels: setup
#666 - Colab pro + failing to predict >2000 residues
Issue -
State: closed - Opened by HBCH1 over 1 year 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 over 1 year ago
- 5 comments
Labels: out of memory
#656 - uniref30_database_path issue
Issue -
State: closed - Opened by limh25 over 1 year ago
- 5 comments
#636 - Running without MSA features
Issue -
State: open - Opened by Gabriel-Ducrocq over 1 year ago
- 7 comments
Labels: usage question
#592 - one error about alphafold,ask for help online
Issue -
State: open - Opened by 285880830 almost 2 years ago
- 2 comments
#573 - DeepMind AlphaFold2 colab notebook already crashes during 3rd party software installation cell
Issue -
State: closed - Opened by MWNautilus almost 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 almost 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 almost 2 years ago
- 2 comments
Labels: feature request
#541 - hhalignment.cpp:3539: MergeMasterSlave error
Issue -
State: closed - Opened by derf0 almost 2 years ago
- 3 comments
Labels: third-party tool
#533 - Installing 3rd party software on Colab not working
Issue -
State: closed - Opened by quockerwodger almost 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 almost 2 years ago
- 4 comments
Labels: usage question
#498 - Unable to initialize backend 'gpu'
Issue -
State: open - Opened by caom92 about 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 about 2 years ago
- 8 comments
Labels: setup
#437 - Faster MSA computations with chunked DBs on Colab
Issue -
State: open - Opened by Meghpal about 2 years ago
- 1 comment
#434 - How to align chain ID of two complexes before running DockQ?
Issue -
State: open - Opened by nonononanana about 2 years ago
- 2 comments
#427 - Use of use_precomputed_msas
Issue -
State: open - Opened by calmip about 2 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 about 2 years ago
- 4 comments
#403 - On docker after some time: No compatible CUDA device is available
Issue -
State: open - Opened by Wolf-Z over 2 years ago
- 8 comments
Labels: docker, cuda
#399 - Parallel execution of MSA tools
Pull Request -
State: open - Opened by fuji8 over 2 years ago
- 13 comments
#392 - 'Out of memory' error
Issue -
State: closed - Opened by wentski over 2 years ago
- 8 comments
Labels: error report, out of memory
#383 - Error in Alpha Fold multimer
Issue -
State: closed - Opened by galshuler over 2 years ago
- 11 comments
Labels: relax
#339 - AF2 non-docker in a cluster enviroment
Issue -
State: closed - Opened by JuergenUniVie over 2 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 over 2 years ago
- 1 comment
#327 - Trouble downloading pdb_mmcif database
Issue -
State: closed - Opened by NMMQ over 2 years ago
- 3 comments
Labels: third-party tool, setup
#321 - Updated Dockerfile to address incompatibilities during setup
Issue -
State: closed - Opened by mbassalbioinformatics over 2 years ago
- 2 comments
Labels: error report, duplicate
#280 - RuntimeError: Jackhmmer failed
Issue -
State: closed - Opened by kdpan over 2 years ago
- 2 comments
#252 - mmCIF output
Issue -
State: open - Opened by brindakv over 2 years ago
- 12 comments
Labels: feature request
#251 - Improper chain IDs when running Multimer model
Issue -
State: open - Opened by nzrandol over 2 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 2 years ago
- 10 comments
Labels: out of memory
#164 - HHblits failed problem
Issue -
State: closed - Opened by Davidswang almost 3 years ago
- 3 comments
#143 - Singularity Definition
Issue -
State: closed - Opened by jdhayes almost 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 almost 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 almost 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 almost 3 years ago
- 9 comments
#97 - RuntimeError: HHblits failed
Issue -
State: closed - Opened by huangjk1103 almost 3 years ago
- 18 comments
Labels: error report
#24 - Non docker setup
Issue -
State: closed - Opened by sanjaysrikakulam almost 3 years ago
- 15 comments
Labels: setup