Ecosyste.ms: Issues

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GitHub / sokrypton/ColabFold issues and pull requests

#579 - Jax dependency Issue

Issue - State: open - Opened by Aradhya-Tripathi 11 months ago - 12 comments

#578 - Model weights download every time when running colabfold_batch

Issue - State: closed - Opened by Nuta0 11 months ago - 2 comments

#577 - Pending. Issue running cell line 331

Issue - State: open - Opened by vincentyao15 11 months ago

#576 - Releases past 1.5.2?

Issue - State: open - Opened by alextruong 11 months ago - 2 comments

#572 - Very minor change to AlphaFold2.ipynb

Pull Request - State: closed - Opened by thachung 12 months ago

#570 - Update utils.py

Pull Request - State: closed - Opened by DimaMolod 12 months ago - 1 comment

#569 - Created using Colaboratory

Pull Request - State: closed - Opened by vsangireddy27 12 months ago

#567 - [BUG] batch error when colabfold_search --use-templates in local search

Issue - State: closed - Opened by lshilab almost 1 year ago - 6 comments

#566 - Replace mmCIF rsync FTP download with AWS CLI download from Amazon S3 PDB Snaphots

Pull Request - State: closed - Opened by teodorpopescuQB about 1 year ago - 4 comments

#565 - Fix template search

Pull Request - State: closed - Opened by PasqM about 1 year ago - 3 comments

#564 - Generating MSAs for chimeric proteins

Issue - State: open - Opened by wcorcoran about 1 year ago - 2 comments

#563 - Colabfold_batch connects to mmseqs server despite msa input

Issue - State: open - Opened by Nuta0 about 1 year ago - 18 comments

#561 - Expecting Multimple model of single sequence run

Issue - State: open - Opened by Hossen-sahadot97 about 1 year ago - 2 comments

#558 - run AMBER relaxation within Docker

Issue - State: closed - Opened by xing-he529 about 1 year ago - 1 comment

#557 - Alphafold_batch

Issue - State: open - Opened by tushar-ahmed about 1 year ago - 3 comments

#556 - Upload box for template does not appear

Issue - State: closed - Opened by NakiaPolidori about 1 year ago - 2 comments

#555 - Running with (A3M input + custom_template_path + is_complex) gives HHsearch error

Issue - State: closed - Opened by huhlim about 1 year ago - 4 comments

#554 - Does sequence order matter when predicting complex

Issue - State: open - Opened by zjq101 about 1 year ago - 1 comment

#553 - Problem using colabfold_search for complexes

Issue - State: closed - Opened by Nuta0 about 1 year ago - 8 comments

#552 - Keep only the most diverse sequences in evey cluster

Issue - State: open - Opened by RobinEllison about 1 year ago - 1 comment

#551 - About MsaServer issue

Issue - State: open - Opened by zhoujingyu13687306871 about 1 year ago - 1 comment

#550 - Questions on large-scale binary complex predictions

Issue - State: open - Opened by Epiphany1029 about 1 year ago

#549 - docker image for cuda11.1?

Issue - State: open - Opened by BinhongLiu about 1 year ago - 41 comments

#548 - MMseqs2 database download link has expired

Issue - State: closed - Opened by yangguang8112 about 1 year ago - 1 comment

#547 - A3M file formatting issue: IndexError: list index out of range

Issue - State: closed - Opened by YousufAKhan about 1 year ago - 5 comments

#545 - Bug fix in models.py

Pull Request - State: closed - Opened by mjag1898 about 1 year ago - 5 comments

#543 - SymbolAlreadyExposedError: Symbol Ones is already exposed as ()

Issue - State: closed - Opened by Saddy48 about 1 year ago - 5 comments

#542 - Tool boxes after google login disappeared

Issue - State: closed - Opened by tomwu1495 about 1 year ago - 6 comments

#540 - AF2 with MMseqs2 ColabFold crash: unable to find SCOPdata

Issue - State: open - Opened by jfbazan about 1 year ago - 6 comments

#539 - AttributeError: module 'jax.ops' has no attribute 'index_add'

Issue - State: closed - Opened by pikkazz about 1 year ago

#538 - Tiny improvements to the help msgs in the search script

Pull Request - State: closed - Opened by gieses about 1 year ago - 2 comments

#537 - RosettaFold2 (WIP) Colab crash

Issue - State: open - Opened by jfbazan about 1 year ago - 2 comments

#536 - AlphaFold Colab (DeepMind version) crash at MSA assembly stage

Issue - State: closed - Opened by jfbazan about 1 year ago - 1 comment

#535 - ESMFold Notebook fails with "No module named openfold" error message

Issue - State: open - Opened by coliva92 about 1 year ago - 5 comments

#534 - Adjust configuration to use PDB100 instead of PDB70 database

Pull Request - State: closed - Opened by teodorpopescuQB about 1 year ago - 2 comments

#532 - error for not enough gpu

Issue - State: open - Opened by benyamin-moraditabar about 1 year ago - 5 comments

#531 - unable to run local colabfold_batch with local mmseqs API

Issue - State: closed - Opened by reyjul about 1 year ago - 2 comments

#529 - AF2 using MMseqs multimer model ranking error?

Issue - State: open - Opened by jfbazan about 1 year ago - 3 comments

#528 - Wrong .a3m format for hmmer

Issue - State: closed - Opened by DimaMolod about 1 year ago - 2 comments

#527 - ColabFold: AlphaFold2 w/ MMseqs2 BATCH Fails to Install Dependencies

Issue - State: closed - Opened by Jzurn-ksu about 1 year ago - 4 comments

#526 - Alphafold-latest

Issue - State: open - Opened by Travis13197 about 1 year ago

#525 - How to read the pae file

Issue - State: open - Opened by FatimaS14 about 1 year ago - 2 comments

#524 - OOM error on Titan X

Issue - State: closed - Opened by rainfieldcn about 1 year ago - 3 comments

#522 - colabfold_batch misuses templates from pdb-hit-file when run locally

Issue - State: open - Opened by bbardiaux about 1 year ago - 1 comment

#521 - Is there a way to specify which GPU to use?

Issue - State: closed - Opened by rainfieldcn about 1 year ago - 1 comment

#520 - Fixed multimer msa not paired if raw_jobname has white spaces

Pull Request - State: closed - Opened by rachelse about 1 year ago - 1 comment

#519 - there is an error whenever I put a pdb file in the custom template.

Issue - State: open - Opened by eirene000 about 1 year ago - 2 comments

#518 - Setup Databases for Multimer A3M file production via colabfold_search

Issue - State: closed - Opened by NickWoodall about 1 year ago - 4 comments

#514 - Update setup_databases.sh

Pull Request - State: open - Opened by nicolang1 about 1 year ago

#507 - Exception: MMseqs2 API is giving errors.

Issue - State: open - Opened by ctarsi over 1 year ago - 5 comments

#495 - Timeout while submitting to MSA server. Retrying...

Issue - State: closed - Opened by shhashem over 1 year ago - 4 comments

#481 - Colabfold MSA server connection error

Issue - State: closed - Opened by alexlevylab over 1 year ago - 14 comments

#409 - Generating template error

Issue - State: open - Opened by Abhishaike almost 2 years ago - 4 comments

#399 - 'Nan' or Not-a-number issue with running ColabFold

Issue - State: open - Opened by jfbazan almost 2 years ago - 14 comments

#387 - running on multiple gpus

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

#381 - How to use templates found by mmseqs

Issue - State: open - Opened by alirezaomidi almost 2 years ago - 5 comments

#356 - Minimization fails with notebook relax_amber.ipynb

Issue - State: open - Opened by EliyaGold about 2 years ago - 6 comments

#325 - Rename `qdb.lookup` so that it will not be removed

Pull Request - State: open - Opened by ZiyaoLi over 2 years ago - 1 comment

#266 - unpackdb stalls

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

#194 - Multimer IPTM score

Issue - State: closed - Opened by xvazquezc almost 3 years ago - 5 comments

#186 - RESOURCE_EXHAUSTED: Out of memory

Issue - State: closed - Opened by a-lewis-acid almost 3 years ago - 1 comment

#130 - Keep Jax compiled

Issue - State: open - Opened by chris-kafka about 3 years ago - 3 comments

#76 - Using AF-Multimer with custom MSA

Issue - State: open - Opened by jessica-andreani about 3 years ago - 10 comments

#35 - Singularity installations?

Issue - State: closed - Opened by shahpnmlab over 3 years ago - 5 comments

#19 - AlphaFold2 protein embedding Notebook as example

Issue - State: open - Opened by ptynecki over 3 years ago - 3 comments