Ecosyste.ms: Issues

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GitHub / KosinskiLab/AlphaPulldown issues and pull requests

#119 - fixed #117

Pull Request - State: closed - Opened by henrywotton over 1 year ago

#118 - Issue with run_multimer_jobs

Issue - State: closed - Opened by sarahemooneyy over 1 year ago - 2 comments
Labels: question

#117 - Fail to align to templates

Issue - State: closed - Opened by Pooryamb over 1 year ago - 2 comments

#116 - Unable to run the singularity image

Issue - State: closed - Opened by matthieu-haudiquet over 1 year ago - 1 comment

#115 - Use obsolete_pdbs_path when using mmseqs2

Pull Request - State: closed - Opened by kttn8769 over 1 year ago - 1 comment

#114 - About protein interface site

Issue - State: closed - Opened by wangxuann1995 over 1 year ago - 1 comment
Labels: question

#113 - Add unittest

Pull Request - State: closed - Opened by henrywotton over 1 year ago

#112 - About reduced db

Issue - State: closed - Opened by Aaronro16 over 1 year ago - 3 comments

#111 - Generating the MSAs by Colabfold

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

#110 - Handel empty template

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

#109 - images of structures not rendering in jupyter

Issue - State: closed - Opened by lauradunphy almost 2 years ago - 3 comments
Labels: bug

#108 - Fix for custom job creation

Pull Request - State: closed - Opened by dennissv almost 2 years ago - 6 comments

#106 - ValueError when calculating some PI-scores

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

#105 - Implement --restart option for run_multimer_jobs.py

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

#104 - Add options for changing msa depth

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

#103 - Add ability of skipping templates

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

#102 - Enable modeling of monomers and their fragments

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

#101 - Add option to skip pairing

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

#100 - Alphafold 2.3.0

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

#99 - Custom model homodimer interaction with other protein input specification

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

#98 - AlphaPulldown 0.22.3 can't run with Alphafold database in Version 2.3.0

Issue - State: closed - Opened by lorethan22 almost 2 years ago - 3 comments

#97 - Error with create_indivisual_features.py

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

#96 - Interpretation of mpDockQ/pDockQ

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

#95 - Improve metadata recording

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

#94 - Unable to generate .pkl (example 1, 1st step)

Issue - State: closed - Opened by ZackLi1984 almost 2 years ago

#93 - Feature request: only run 1 set of model params instead of all 5?

Issue - State: closed - Opened by rlawr almost 2 years ago - 7 comments

#92 - cannot find .cif file during feature generation

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

#91 - Improve flags handling?

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

#90 - output_dir is merged with protein description?

Issue - State: closed - Opened by DimaMolod almost 2 years ago - 5 comments

#89 - FileNotFoundError: [Errno 2] No such file or directory: 'hhsearch': 'hhsearch'

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

#88 - fixed #82

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

#87 - run_get_good_pae.sh "jobs" data missing when computing pi_score

Issue - State: closed - Opened by SchwarzMarek almost 2 years ago - 11 comments

#85 - Pvalue in output csv table

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

#84 - GPU usage in create_individual_features.py

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

#83 - Issue 72

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

#82 - Improve auto-creating output directory in check_output_dir

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

#81 - Very slow compile error

Issue - State: closed - Opened by mpm896 about 2 years ago - 7 comments

#80 - Error with run_multimer_jobs.py

Issue - State: closed - Opened by mpm896 about 2 years ago - 5 comments

#79 - Modeling entire protein chain based on fragment multimer model

Issue - State: closed - Opened by mpm896 about 2 years ago - 1 comment

#78 - added a try-exception block fixe #71

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

#77 - Error with run_multimer_jobs.py when using MMseqs2

Issue - State: closed - Opened by gretabellinzona about 2 years ago - 10 comments

#76 - unable to execute create_individual_features.py to compute MSA

Issue - State: closed - Opened by sarbanid about 2 years ago - 6 comments

#75 - why python==3.7.* ?

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

#74 - When I create predictions_with_good_interpae.csv, there is some problems

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

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

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

#72 - Wrong paths passed to make_mmseq_features

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

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

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

#70 - prepare_seq_names.py not working?

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

#69 - Update manuals

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

#68 - --use_precomputed_msas=False is confusing here

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

#67 - Mmseq2

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

#66 - Recalculate template features only in local mmseqs2 mode

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

#65 - A small typo ;-)

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

#64 - Adding templates for local mmseqs2 mode here?

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

#63 - Where does it read template alignments?

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

#62 - data_dir really not needed?

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

#61 - Restructuring the MSA generation to include MMseqs2

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

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

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

#59 - Mmseq2

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

#58 - --max_template_date with MMSeqs2

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

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

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

#56 - modeling of higher-order oligomers question

Issue - State: closed - Opened by pillepalle123 about 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 over 2 years ago
Labels: enhancement

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

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

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

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

#41 - jackhmmer fails to run

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

#40 - seq_index is not working

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

#39 - Create LICENSE

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

#38 - Readme2

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

#37 - Update example_1.md

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

#36 - Readme

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

#35 - Issue 31

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

#32 - Remove redunancies from predict_structure.py

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

#31 - Remove p-value from analysis table

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

#27 - Use correct residue numbering in the PAE plots

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

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

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

#9 - Add option to zip MSA files

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

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

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