Ecosyste.ms: Issues

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GitHub / KosinskiLab/AlphaPulldown issues and pull requests

#73 - Permission denied. I do not know why always put this error?

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

#72 - Wrong paths passed to make_mmseq_features

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

#71 - Improve auto-creating output directory in create_individual_features.py

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

#70 - prepare_seq_names.py not working?

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

#69 - Update manuals

Pull Request - State: closed - Opened by henrywotton almost 2 years ago

#68 - --use_precomputed_msas=False is confusing here

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

#67 - Mmseq2

Pull Request - State: closed - Opened by henrywotton almost 2 years ago

#66 - Recalculate template features only in local mmseqs2 mode

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

#65 - A small typo ;-)

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

#64 - Adding templates for local mmseqs2 mode here?

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

#63 - Where does it read template alignments?

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

#62 - data_dir really not needed?

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

#61 - Restructuring the MSA generation to include MMseqs2

Pull Request - State: closed - Opened by jkosinski almost 2 years ago

#60 - Add a warning of not overloading the remote server

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

#59 - Mmseq2

Pull Request - State: closed - Opened by henrywotton almost 2 years ago

#58 - --max_template_date with MMSeqs2

Issue - State: closed - Opened by jkosinski almost 2 years ago - 3 comments
Labels: question

#57 - The option should be --mmseqs2 instead of --mmseq2

Issue - State: closed - Opened by jkosinski almost 2 years ago
Labels: invalid

#56 - modeling of higher-order oligomers question

Issue - State: closed - Opened by pillepalle123 almost 2 years ago - 6 comments

#55 - `--model_preset` flag is not used

Issue - State: open - Opened by swanss about 2 years ago - 9 comments

#54 - Interpretation of output

Issue - State: closed - Opened by nduan1 about 2 years ago - 3 comments

#53 - Add option to not pair MSAs in run_multimer_jobs.py

Pull Request - State: closed - Opened by swanss about 2 years ago - 1 comment

#52 - Installing the project as a package in developer mode

Issue - State: closed - Opened by swanss about 2 years ago - 4 comments

#51 - Unable to initialize backend 'tpu_driver'

Issue - State: closed - Opened by nduan1 about 2 years ago - 4 comments

#50 - Create requirements.txt

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

#49 - How to speed up the first step for model prediction?

Issue - State: closed - Opened by nduan1 about 2 years ago - 3 comments

#48 - CUDA out of memory error when running multimer

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

#46 - Cleanup objects

Pull Request - State: closed - Opened by henrywotton about 2 years ago

#45 - update alpha-analysis.sif

Pull Request - State: closed - Opened by henrywotton about 2 years ago

#44 - Improve pi_score folder management

Issue - State: closed - Opened by jkosinski about 2 years ago
Labels: enhancement

#43 - A question about the seq_index argument in job array mode

Issue - State: closed - Opened by swanss about 2 years ago - 1 comment

#42 - Requesting feature: ability to skip MSA generation step

Issue - State: open - Opened by swanss about 2 years ago - 1 comment
Labels: enhancement

#41 - jackhmmer fails to run

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

#40 - seq_index is not working

Issue - State: closed - Opened by henrywotton about 2 years ago - 1 comment
Labels: bug

#39 - Create LICENSE

Pull Request - State: closed - Opened by jkosinski about 2 years ago

#38 - Readme2

Pull Request - State: closed - Opened by jkosinski about 2 years ago

#37 - Update example_1.md

Pull Request - State: closed - Opened by jkosinski about 2 years ago

#36 - Readme

Pull Request - State: closed - Opened by jkosinski about 2 years ago

#35 - Issue 31

Pull Request - State: closed - Opened by henrywotton about 2 years ago

#32 - Remove redunancies from predict_structure.py

Issue - State: closed - Opened by jkosinski about 2 years ago - 1 comment

#31 - Remove p-value from analysis table

Issue - State: closed - Opened by jkosinski about 2 years ago

#27 - Use correct residue numbering in the PAE plots

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

#15 - Add info to the manual that relax is not run

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

#9 - Add option to zip MSA files

Issue - State: closed - Opened by jkosinski about 2 years ago - 2 comments
Labels: enhancement

#5 - Create instructions how to prepare MSAs with ColabFold?

Issue - State: closed - Opened by jkosinski about 2 years ago