Ecosyste.ms: Issues

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GitHub / KosinskiLab/AlphaPulldown issues and pull requests

#179 - Duplicated to_bio?

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

#178 - Move it out of create_arguments() function

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

#177 - Add mmseqs2 info

Issue - State: closed - Opened by jkosinski about 1 year ago - 5 comments
Labels: enhancement

#176 - Add Alphapulldown token to mmseqs2 request

Issue - State: closed - Opened by jkosinski about 1 year ago - 1 comment
Labels: enhancement

#175 - Database description difference APD vs. AF

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

#174 - Too many atoms?

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

#173 - alpha-analysis.sif - no csv output

Issue - State: closed - Opened by JtheBAB about 1 year ago - 7 comments
Labels: enhancement

#172 - issue on running mmseqs2 remotely

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

#170 - Output.ipynb does not work

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

#169 - error encountered with alpha-analysis.sif

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

#167 - True multimer

Pull Request - State: closed - Opened by DimaMolod about 1 year ago
Labels: enhancement

#165 - Error in the execution of Feature 2

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

#164 - "af2_plots @ b5b96c8" seems inaccessible

Issue - State: closed - Opened by kimcho452 about 1 year ago - 5 comments

#163 - Dealing with disordered proteins

Issue - State: closed - Opened by 0Telepathetic0 about 1 year ago - 1 comment

#162 - Problem Creating CSV Output: KeyError 'jobs'

Issue - State: closed - Opened by teaninja about 1 year ago - 17 comments

#161 - KeyError: 'P78344.pkl'

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

#156 - Run using only mmseqs/colabfold

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

#155 - Proper naming for alpha-analysis.sif

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

#154 - "Could not find the template sequence" and "must be real number, not NoneType"

Issue - State: closed - Opened by nduan1 over 1 year ago - 4 comments

#153 - Save mmCIF output files

Issue - State: closed - Opened by jkosinski over 1 year ago - 1 comment
Labels: enhancement

#152 - Alphafold databases when running mmseqs2 locally

Issue - State: closed - Opened by susiegriggo over 1 year ago - 8 comments

#151 - Develop readme

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

#150 - Create Developing.md

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

#149 - Move and organize readme files and png files in a doc directory

Issue - State: closed - Opened by jkosinski over 1 year ago - 1 comment
Labels: documentation

#148 - Add remote jupyter server link

Issue - State: closed - Opened by jkosinski over 1 year ago - 1 comment
Labels: documentation

#147 - Updating AlphaPulldown

Issue - State: closed - Opened by mpm896 over 1 year ago - 1 comment

#146 - missing information in notebook file

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

#145 - Installation does not work on Macbook with M2

Issue - State: closed - Opened by jkosinski over 1 year ago - 2 comments
Labels: bug

#143 - Merged main

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

#142 - fixed ranked plddt error

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

#141 - Plotting interaction network

Issue - State: open - Opened by mpm896 over 1 year ago - 1 comment
Labels: enhancement

#140 - seq_index Error

Issue - State: closed - Opened by mbaddoo over 1 year ago - 5 comments

#139 - Update README.md

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

#138 - Update the add-unifold branch

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

#137 - af2plots missing and not installed?

Issue - State: closed - Opened by jkosinski over 1 year ago - 3 comments
Labels: bug

#136 - Fix paths in test_predict_structure.py

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

#135 - Fix random seed

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

#134 - Organise submodules

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

#133 - Adding pulldown mode running on CPU

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

#132 - Running on low VRAM (8GB) GPU

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

#131 - Pulldown error on WSL2

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

#130 - Independently run MSA prediction?

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

#129 - np.int and np.object error

Issue - State: closed - Opened by remybonnav over 1 year ago - 9 comments

#128 - Fix 120

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

#127 - How to run Pulldown on defined "candidates" list without AlphaFold Directory

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

#126 - tensorflow problem

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

#125 - How to evaluate interaction for more than two proteins

Issue - State: closed - Opened by SchwarzMarek over 1 year ago - 5 comments
Labels: enhancement

#124 - Singularity image does not work with alphafold results.

Issue - State: closed - Opened by tony9959 over 1 year ago - 1 comment

#123 - Recommend more specific version of `PDBfixer`

Issue - State: closed - Opened by deniskristak over 1 year ago - 1 comment
Labels: documentation

#122 - Fix relax and resume

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

#121 - Fix relax and add multimer job resume

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

#120 - KeyError: 'template_confidence_scores'

Issue - State: closed - Opened by Pooryamb over 1 year ago - 7 comments
Labels: bug

#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 over 1 year ago

#109 - images of structures not rendering in jupyter

Issue - State: closed - Opened by lauradunphy over 1 year ago - 3 comments
Labels: bug

#108 - Fix for custom job creation

Pull Request - State: closed - Opened by dennissv over 1 year ago - 6 comments

#106 - ValueError when calculating some PI-scores

Issue - State: closed - Opened by EricLMiller over 1 year ago - 6 comments

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

Issue - State: closed - Opened by jkosinski over 1 year ago
Labels: enhancement

#104 - Add options for changing msa depth

Issue - State: closed - Opened by jkosinski over 1 year ago - 1 comment
Labels: enhancement

#103 - Add ability of skipping templates

Issue - State: closed - Opened by jkosinski over 1 year ago - 3 comments
Labels: enhancement

#102 - Enable modeling of monomers and their fragments

Issue - State: closed - Opened by jkosinski over 1 year ago - 1 comment
Labels: enhancement

#101 - Add option to skip pairing

Issue - State: closed - Opened by jkosinski over 1 year ago - 1 comment
Labels: enhancement

#100 - Alphafold 2.3.0

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

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

Issue - State: closed - Opened by SchwarzMarek over 1 year 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 over 1 year 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 almost 2 years ago - 2 comments

#84 - GPU usage in create_individual_features.py

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

#83 - Issue 72

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

#82 - Improve auto-creating output directory in check_output_dir

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

#81 - Very slow compile error

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

#80 - Error with run_multimer_jobs.py

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

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

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

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

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

#77 - Error with run_multimer_jobs.py when using MMseqs2

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

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

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

#75 - why python==3.7.* ?

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

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

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