Ecosyste.ms: Issues

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GitHub / KosinskiLab/AlphaPulldown issues and pull requests

#454 - Why limiting output directory to 100?

Issue - State: closed - Opened by jkosinski 21 days ago - 6 comments

#453 - run_multimer_jobs.py "check_empty_templates error"

Issue - State: closed - Opened by Prospero912 22 days ago - 2 comments

#452 - Update doc for rename_colab_search_a3m.py

Pull Request - State: closed - Opened by jkosinski 22 days ago - 2 comments

#450 - Use https instead of ssh in `.gitmodules`

Pull Request - State: open - Opened by shermanlo77 23 days ago - 4 comments

#449 - snakemake from main branch crashes on prediction

Issue - State: closed - Opened by jkosinski 27 days ago - 1 comment
Labels: bug

#448 - Installation from pip not functional for predictions?

Issue - State: closed - Opened by jkosinski 27 days ago - 4 comments
Labels: invalid

#447 - Update AlphaLink2 citation

Issue - State: open - Opened by jkosinski 27 days ago
Labels: documentation

#446 - Fix spaces after backslashes in commands

Pull Request - State: closed - Opened by jkosinski 27 days ago

#444 - Issue while installing fold_analysis

Issue - State: closed - Opened by gabrielpan147 28 days ago - 1 comment

#443 - Update PyPi version for the Biopython fix?

Issue - State: closed - Opened by jkosinski 28 days ago - 1 comment
Labels: bug

#442 - Convert setup.py to pyproject.toml

Pull Request - State: closed - Opened by DimaMolod about 1 month ago

#441 - Improve docs

Pull Request - State: open - Opened by DimaMolod about 1 month ago - 1 comment

#440 - Clean dependencies

Pull Request - State: closed - Opened by DimaMolod about 1 month ago

#439 - Error with singularity during installation

Issue - State: open - Opened by ebettler about 1 month ago - 6 comments

#438 - Shouldn't tests be run for user installation too?

Issue - State: closed - Opened by jkosinski about 1 month ago - 1 comment
Labels: question

#437 - Not getting binaries in path...

Issue - State: closed - Opened by jkosinski about 1 month ago - 3 comments
Labels: help wanted

#436 - install_jax

Pull Request - State: closed - Opened by DimaMolod about 1 month ago

#435 - Make the script executable is not necessary

Issue - State: open - Opened by jkosinski about 1 month ago
Labels: documentation

#434 - Update CCP4 for non-snakemake

Issue - State: open - Opened by jkosinski about 1 month ago
Labels: documentation

#433 - Instructions how to update AP snakemake

Issue - State: open - Opened by jkosinski about 1 month ago - 2 comments
Labels: documentation

#432 - Trying to make the CCP4 install clearer

Pull Request - State: closed - Opened by jkosinski about 1 month ago

#431 - File name too long owing to folder nomenclature

Issue - State: closed - Opened by ordavies about 1 month ago - 3 comments

#429 - Update manual

Pull Request - State: closed - Opened by gilep about 1 month ago

#428 - Add ColabFold backend

Issue - State: open - Opened by jkosinski about 1 month ago
Labels: enhancement

#427 - Some candidates in the prediction step lead to the following error :

Issue - State: open - Opened by ThisIsIt42 about 1 month ago - 4 comments

#426 - fix-423

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

#425 - unnecessary step in ccp4 installation?

Issue - State: closed - Opened by jkosinski about 2 months ago
Labels: documentation

#424 - Wrong fold_analysis.sif filename?

Issue - State: closed - Opened by jkosinski about 2 months ago
Labels: documentation

#423 - Found unknown key in 'other' errors

Issue - State: closed - Opened by jkosinski about 2 months ago - 4 comments
Labels: invalid

#420 - Suggest how to run the snakemake pipeline in the background

Issue - State: open - Opened by jkosinski about 2 months ago
Labels: documentation

#418 - Documentation for other options

Issue - State: open - Opened by jkosinski about 2 months ago
Labels: documentation

#417 - PI score calculation failed

Issue - State: closed - Opened by ewysocka about 2 months ago - 4 comments

#416 - Update github_actions.yml

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

#415 - Put it before Execution

Issue - State: closed - Opened by jkosinski about 2 months ago
Labels: documentation

#414 - Rephrase analysis install instruction in README.md

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

#413 - Add instructions how to use existing features

Issue - State: open - Opened by jkosinski about 2 months ago
Labels: documentation

#412 - Add how to install the latest version too

Issue - State: closed - Opened by jkosinski about 2 months ago
Labels: documentation

#411 - Add example how to specify multiple residue ranges

Issue - State: open - Opened by jkosinski about 2 months ago
Labels: documentation

#410 - Remove ccp4 and upgrade biopython

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

#409 - Move submodules one level deeper to avoid conflicts with globally installed AF,AL,CF

Issue - State: open - Opened by DimaMolod about 2 months ago
Labels: enhancement

#408 - Compatible installation with python 3.11?

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

#407 - Remove cctbx from dependencies

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

#406 - Can I use AlphaPullDown for 5K proteins?

Issue - State: closed - Opened by Rohit-Satyam about 2 months ago - 6 comments

#405 - Fix analysis pipeline

Pull Request - State: closed - Opened by DimaMolod 2 months ago

#404 - Remove unused code, clean code/tests

Pull Request - State: closed - Opened by DimaMolod 3 months ago

#401 - Meaning of binding_energy in result table

Issue - State: closed - Opened by jansteinkuehler 3 months ago - 1 comment

#398 - jax installation version issue

Issue - State: closed - Opened by jansteinkuehler 3 months ago - 1 comment
Labels: documentation

#396 - Postprocessing

Pull Request - State: closed - Opened by DimaMolod 4 months ago

#393 - Updated manual

Pull Request - State: closed - Opened by DimaMolod 4 months ago

#392 - Fix noncritical bugs

Pull Request - State: closed - Opened by DimaMolod 4 months ago

#391 - question: correct pipeline for mmseqs alignments in alphapulldown?

Issue - State: closed - Opened by gieses 4 months ago - 5 comments
Labels: bug

#390 - Remove result pickles

Issue - State: closed - Opened by jkosinski 4 months ago - 1 comment
Labels: bug

#387 - Change re for finding PAE.png plots

Pull Request - State: closed - Opened by DimaMolod 4 months ago - 1 comment

#386 - Fix KeyError 'iptm+ptm' not found in analysis pipeline

Pull Request - State: closed - Opened by DimaMolod 4 months ago - 1 comment

#385 - create_notebook doesn't work on AlphaPulldown 2.0b?

Issue - State: closed - Opened by gebauer 4 months ago - 8 comments

#384 - Remove a Protein object from result.pkl during postprocessing

Pull Request - State: closed - Opened by DimaMolod 4 months ago - 5 comments

#381 - jax error when create_notebook.py is run

Issue - State: closed - Opened by BismahGhafoor 5 months ago - 4 comments

#380 - Computing MSA takes long time

Issue - State: closed - Opened by aaposaav 5 months ago

#379 - output jupyter notebook is empty

Issue - State: closed - Opened by sheng19331 5 months ago - 2 comments

#378 - rename_colab_search_a3m.py does something unintended

Issue - State: closed - Opened by IwanParf 5 months ago - 5 comments

#377 - Rebase Konstantin's branch

Pull Request - State: closed - Opened by dingquanyu 5 months ago

#376 - Problem with MSA for Q6DI86

Issue - State: closed - Opened by poojaparameswaran99 5 months ago - 2 comments

#375 - Update pulldown.dockerfile

Pull Request - State: closed - Opened by dingquanyu 5 months ago

#374 - Added mmseqs2 template features to chopped objects

Pull Request - State: closed - Opened by dingquanyu 5 months ago

#373 - Merging individual monomer MSAs for multimer prediction

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

#372 - Update parse_fold

Pull Request - State: closed - Opened by dingquanyu 5 months ago - 1 comment

#371 - Fix 362

Pull Request - State: closed - Opened by dingquanyu 5 months ago - 5 comments

#370 - create_indvidual_features.py

Issue - State: closed - Opened by poojaparameswaran99 5 months ago - 3 comments

#368 - Fix 367

Pull Request - State: closed - Opened by dingquanyu 5 months ago - 6 comments

#367 - 'ranking_confidence' is not in the result.pkl file after the update

Issue - State: closed - Opened by DimaMolod 6 months ago - 10 comments

#366 - Rearange backend initialisation

Pull Request - State: closed - Opened by dingquanyu 6 months ago - 2 comments

#365 - Convert predicted models to modelcif

Pull Request - State: closed - Opened by DimaMolod 6 months ago

#364 - Update libffi version

Pull Request - State: closed - Opened by dingquanyu 6 months ago - 4 comments

#363 - Clean duplicating functions/ redundant code

Issue - State: closed - Opened by DimaMolod 6 months ago - 1 comment

#362 - Use DEFINE_list for model_names flag

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

#361 - Fix 344

Pull Request - State: closed - Opened by dingquanyu 6 months ago

#360 - Updated container creation scheme

Pull Request - State: closed - Opened by maurerv 6 months ago - 2 comments

#359 - Runtime of each prediction

Issue - State: closed - Opened by what-is-what 6 months ago - 1 comment

#358 - GPU seems not working when run_multimer_jobs.py

Issue - State: closed - Opened by HUST6324 6 months ago - 5 comments

#356 - More exception in analysis pipeline

Pull Request - State: closed - Opened by dingquanyu 6 months ago

#355 - Improve resume predictions

Pull Request - State: closed - Opened by DimaMolod 6 months ago - 4 comments

#354 - 343 replace this with non cctbx solution

Pull Request - State: closed - Opened by gchojnowski 6 months ago - 2 comments

#353 - Improve resume predictions

Issue - State: closed - Opened by DimaMolod 6 months ago - 1 comment

#352 - Multiple feature directories

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

#351 - Update example_1.md

Pull Request - State: closed - Opened by B0r1sD 6 months ago - 2 comments

#350 - jackhammer error running test

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

#349 - Add again --dry_run flag

Pull Request - State: closed - Opened by DimaMolod 6 months ago - 1 comment

#347 - Now allow it to parse pLDDT values from bfactor

Pull Request - State: closed - Opened by dingquanyu 6 months ago

#346 - Group unittests

Pull Request - State: closed - Opened by dingquanyu 6 months ago - 1 comment

#345 - Update alphalink backend

Pull Request - State: closed - Opened by dingquanyu 6 months ago

#344 - singularity error

Issue - State: closed - Opened by polya18 6 months ago - 21 comments

#343 - Replace this with non-cctbx solution

Issue - State: closed - Opened by jkosinski 6 months ago - 7 comments

#342 - run_multimer_jobs issue

Issue - State: closed - Opened by J-Held 6 months ago - 5 comments

#341 - Running calculate_mpdockq.py with only PDB

Issue - State: closed - Opened by busrasavas 7 months ago - 1 comment

#340 - Add dropout

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

#339 - GPU not working when run_multimer_jobs.py

Issue - State: open - Opened by polya18 7 months ago - 3 comments