Ecosyste.ms: Issues

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GitHub / sokrypton/ColabFold issues and pull requests

#672 - MMSeqsGPU support

Pull Request - State: closed - Opened by kierandidi about 1 month ago - 2 comments

#670 - What should I do if I just want to use colabfold_search with mmseqs-gpu?

Issue - State: closed - Opened by TheChosenOneJG about 1 month ago - 2 comments

#669 - Boltz only runs test 5c831

Issue - State: open - Opened by jenchem-ot about 1 month ago

#668 - Alt dockerfile

Pull Request - State: closed - Opened by BrandonFrenz about 2 months ago - 1 comment

#667 - During run Prediction

Issue - State: open - Opened by cjwilli98 about 2 months ago - 2 comments

#666 - Actifptm

Pull Request - State: closed - Opened by gezmi about 2 months ago

#665 - Local MSA results different from MSA server

Issue - State: open - Opened by sangyeon-hits about 2 months ago - 4 comments

#664 - Intermittent timeouts from MSA server

Issue - State: open - Opened by rachitk 2 months ago - 17 comments

#663 - Logic error in error handling for MMSeqs2 server connection

Issue - State: open - Opened by tristanic 2 months ago - 1 comment

#662 - Add alphafold 3

Issue - State: open - Opened by wswxyq 2 months ago - 1 comment

#661 - Use AlphaFold2 ptm for multimer chain-break prediction

Issue - State: closed - Opened by sirius777coder 2 months ago - 11 comments

#659 - Unable to see Memory usage on MMSeq Server

Issue - State: open - Opened by amani-acog 2 months ago

#658 - 403 Forbidden message from API

Issue - State: open - Opened by james-vincent 2 months ago - 4 comments

#656 - No module named 'pdbfixer' in relax_amber.ipynb

Issue - State: closed - Opened by hajnal-adam 3 months ago - 5 comments

#652 - Issues using forked alphafold for modifed colabfold

Issue - State: open - Opened by michaelhla 4 months ago - 3 comments

#650 - MSA on local machine?

Issue - State: open - Opened by GXcells 4 months ago - 1 comment

#649 - MMseq2 API error

Issue - State: open - Opened by GISTAL 5 months ago

#646 - Timing out when attempting to make a prediction?

Issue - State: open - Opened by rachitk 5 months ago - 4 comments

#645 - Limitations for template selection

Issue - State: closed - Opened by GISTAL 5 months ago - 1 comment

#644 - Custom template issue

Issue - State: open - Opened by PDEPMC 5 months ago - 2 comments

#643 - run prediction error

Issue - State: open - Opened by gmestrallet 6 months ago

#639 - Support `aarch64` with pip

Pull Request - State: closed - Opened by wahabk 6 months ago - 3 comments

#638 - LLVM Error on `aarch64` container

Issue - State: closed - Opened by wahabk 6 months ago - 2 comments

#637 - Colabfold install on `aarch64` with GPU support

Issue - State: closed - Opened by wahabk 6 months ago - 3 comments

#635 - Trying to run ColabFold v1.5.2

Issue - State: open - Opened by msafranchik1994 6 months ago - 2 comments

#633 - Add chain_iptm and ptm_matrix saving in the json file.

Pull Request - State: open - Opened by samuelmurail 7 months ago

#632 - Data privacy policy

Issue - State: open - Opened by iRove108 7 months ago

#631 - removed ,<3.12 for causing installation issues

Pull Request - State: closed - Opened by KeaunAmani 7 months ago - 1 comment

#630 - AlphaFold2_advanced.ipynb numpy error

Issue - State: open - Opened by justinecwilliams 7 months ago - 2 comments

#629 - How does not apply MSA server to run ColabFold

Issue - State: open - Opened by 15019669985 7 months ago - 2 comments

#627 - Issue when using template mode

Issue - State: closed - Opened by samuelmurail 8 months ago - 7 comments

#626 - Clarification on MSA server RAM requirements

Issue - State: closed - Opened by puddleglum56 8 months ago - 2 comments

#625 - multimeres not working with local mmseqs API

Issue - State: closed - Opened by reyjul 8 months ago - 11 comments

#623 - ModuleNotFoundError BiopythonDeprecationWarning

Issue - State: open - Opened by bai717273 8 months ago - 3 comments

#622 - Fixing biopython compatibility issue by reverting to 1.81

Pull Request - State: closed - Opened by sid-betalol 8 months ago - 1 comment

#620 - Two MSA results in --msa-only output

Issue - State: open - Opened by NooraAz 9 months ago

#619 - install dependencies error

Issue - State: closed - Opened by norsedrunkensailor 9 months ago - 4 comments

#618 - Timeout while submitting to MSA server

Issue - State: open - Opened by zhangjuan233 9 months ago - 8 comments

#617 - ColabFold custom PDB upload

Issue - State: open - Opened by mjemmett 9 months ago - 1 comment

#616 - ColabFold 1.5.5 / AF2 using MMSeqs2 crash due to MMSeqs2 API errors

Issue - State: closed - Opened by jfbazan 9 months ago - 1 comment

#615 - Error extracting the uniref30

Issue - State: open - Opened by ahof1704 9 months ago

#614 - add environmental pairing feature

Pull Request - State: closed - Opened by endixk 9 months ago

#613 - AlphaFold2_batch, MSA single_sequence, use_templates

Issue - State: open - Opened by msimchi 9 months ago

#610 - Error in Local Template Search

Issue - State: open - Opened by GCS-ZHN 9 months ago

#609 - colabfold_search failed on custom sequence database

Issue - State: open - Opened by qiyifei1 9 months ago - 3 comments

#608 - Relax_amber notebook

Issue - State: open - Opened by Jameel9 9 months ago

#607 - checkpointing in job submissions

Issue - State: open - Opened by apal6 9 months ago

#606 - Timeout api.colabfold.com server

Issue - State: open - Opened by rukibuki 9 months ago - 16 comments

#605 - General refactoring for increased modularity and separation of concerns

Pull Request - State: open - Opened by alexpBCR 9 months ago - 3 comments

#603 - RosettaFold2 Colab crashing at end of prediction run

Issue - State: open - Opened by jfbazan 9 months ago - 2 comments

#602 - "Attributer Error" in Cell 4 AlphaFold.ipynb

Issue - State: closed - Opened by tillenglert 9 months ago - 2 comments

#598 - multimers : model 1model 2 etc

Issue - State: closed - Opened by GXcells 10 months ago

#597 - Fix dockerfile not to fail `docker build`

Pull Request - State: open - Opened by eunos-1128 10 months ago

#594 - Index out of range during the display of 3D structure.

Issue - State: open - Opened by Nikromet 10 months ago - 2 comments

#593 - Supplying alternative model weights

Issue - State: closed - Opened by dthorburn 10 months ago - 7 comments

#592 - Implement initial guess feature

Pull Request - State: open - Opened by Poko18 10 months ago - 2 comments

#590 - Add Initial Guess Feature

Pull Request - State: closed - Opened by Poko18 10 months ago

#588 - Difference between AF and AF advanced

Issue - State: closed - Opened by avinashkarkada 10 months ago

#587 - No info in output.cvs LazyAF colab AlphaFold2-Multimer

Issue - State: open - Opened by pauldambio 10 months ago - 1 comment

#586 - evoformer embeddings

Issue - State: open - Opened by adrienchaton 10 months ago - 1 comment

#585 - Error in using custom mode and pdb file

Issue - State: open - Opened by mialaudele 10 months ago - 1 comment

#583 - can't reproduce results with same a3m file.

Issue - State: closed - Opened by jzhanghzau 11 months ago - 1 comment

#582 - Cannot find output PDB files

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

#581 - pdb100_230517_seq does not exist issue

Issue - State: open - Opened by rakeshr10 11 months ago - 3 comments

#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