Ecosyste.ms: Issues

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GitHub / KosinskiLab/AlphaPulldown issues and pull requests

#338 - Update documentation request

Issue - State: closed - Opened by Clockris 7 months ago - 2 comments

#337 - Too many proteins in one interaction ?

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

#336 - Add generation of JSON for AlphaFold server

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

#334 - using several GPUs on a single workstation

Issue - State: open - Opened by errinaceus 7 months ago - 1 comment

#333 - Improve pdb_analyser.py

Pull Request - State: closed - Opened by DimaMolod 7 months ago - 2 comments

#330 - Fix interface measurements in the analysis pipeline

Pull Request - State: closed - Opened by dingquanyu 7 months ago - 3 comments

#329 - pi-score outputs

Issue - State: closed - Opened by salomonssonj 7 months ago - 7 comments

#328 - Multiple mmts

Pull Request - State: closed - Opened by DimaMolod 7 months ago - 3 comments

#327 - Fix 292 and singularity image

Pull Request - State: closed - Opened by dingquanyu 7 months ago

#323 - predictions_with_good_interpae.csv

Issue - State: closed - Opened by DimaMolod 7 months ago
Labels: bug

#322 - Different behavior of the all_vs_all mode in AlphaPulldown 2.0.0 beta v2?

Issue - State: closed - Opened by TM-Hamm 7 months ago - 9 comments

#321 - update tests and fixed create_notebook

Pull Request - State: closed - Opened by dingquanyu 7 months ago

#320 - Flash attention?

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

#319 - operands could not be broadcast together with shapes - MMSEQ2

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

#318 - Update tests

Pull Request - State: closed - Opened by dingquanyu 8 months ago

#317 - Snakemake docker

Pull Request - State: closed - Opened by DimaMolod 8 months ago

#316 - Path output alpha-analysis.sif

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

#313 - Version2

Pull Request - State: closed - Opened by DimaMolod 8 months ago - 9 comments

#312 - Version2 beta v1 issues

Issue - State: closed - Opened by dingquanyu 8 months ago

#311 - Add interface PAE and plddt calculation to anlaysis pipeline

Pull Request - State: closed - Opened by dingquanyu 8 months ago - 4 comments

#310 - database setup - HHblits reference

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

#309 - rebase openfold branch

Pull Request - State: closed - Opened by dingquanyu 8 months ago

#308 - Manuals 2.0 beta

Pull Request - State: closed - Opened by dingquanyu 8 months ago - 5 comments

#307 - Fix292, update analysis pipeline singularity files

Pull Request - State: closed - Opened by dingquanyu 8 months ago

#306 - Update alphafold_backend.py

Pull Request - State: closed - Opened by DimaMolod 8 months ago

#305 - Fix padding

Pull Request - State: closed - Opened by dingquanyu 8 months ago

#304 - fixed an issue in af2-like coloring by plddt

Pull Request - State: closed - Opened by gchojnowski 8 months ago

#303 - Backend revision

Pull Request - State: closed - Opened by dingquanyu 8 months ago - 6 comments

#301 - merge updates on indents and function cleaning

Pull Request - State: closed - Opened by dingquanyu 8 months ago

#300 - Merge Dima patches to jit-jobs first

Pull Request - State: closed - Opened by dingquanyu 8 months ago

#299 - Pad input features from different prediction jobs to a universal desired shapes

Pull Request - State: closed - Opened by dingquanyu 8 months ago - 4 comments

#298 - Update setup.cfg: setting tensorflow>=2.14.0 leads to incompatible cuda

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

#297 - Reopening PR

Pull Request - State: closed - Opened by DimaMolod 8 months ago - 3 comments

#296 - Setting tensorflow>=2.14.0 leads to incompatible cuda

Issue - State: closed - Opened by kashyapchhatbar 8 months ago - 1 comment

#295 - Revert "Dima small patches"

Pull Request - State: closed - Opened by dingquanyu 8 months ago

#294 - num_predictions_per_model

Issue - State: closed - Opened by hqdream 9 months ago - 3 comments

#293 - How to run with reduced_dbs

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

#292 - KeyError: 'template_confidence_scores'

Issue - State: closed - Opened by Qrouger 9 months ago - 13 comments

#291 - Dima small patches

Pull Request - State: closed - Opened by DimaMolod 9 months ago - 7 comments

#290 - alpha-analysis.sif can not process larger models

Issue - State: closed - Opened by teaninja 9 months ago - 5 comments
Labels: bug

#289 - added standard alphafold database coloring to notebook displays

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

#288 - Fix 223 282

Pull Request - State: closed - Opened by dingquanyu 9 months ago - 1 comment

#287 - ValueError: operands could not be broadcast together

Issue - State: closed - Opened by Stigimoloch 9 months ago - 5 comments

#285 - Reorganise structure of the package

Pull Request - State: closed - Opened by dingquanyu 9 months ago - 15 comments

#284 - Update objects.py and unittest on objects.py

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

#283 - Rebase update-truemultimer

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

#282 - FLAGS.use_gpu_relax not passed to predict()

Issue - State: closed - Opened by jkosinski 9 months ago

#281 - Merging error if pair_msa=False when executing pair_and_merge

Issue - State: closed - Opened by dingquanyu 9 months ago
Labels: bug

#280 - New.

Pull Request - State: closed - Opened by DimaMolod 9 months ago - 2 comments

#279 - KeyError when executing run_get_good_pae.sh

Issue - State: closed - Opened by maurerv 9 months ago - 1 comment
Labels: bug

#278 - Update predict_structure.py

Pull Request - State: closed - Opened by DimaMolod 9 months ago - 1 comment

#277 - Fix 9

Pull Request - State: closed - Opened by dingquanyu 9 months ago - 1 comment

#276 - Consider removing extra information from model pkl immediately before saving them

Issue - State: closed - Opened by jkosinski 9 months ago - 2 comments
Labels: enhancement

#275 - Parallise analysis pipeline

Pull Request - State: closed - Opened by dingquanyu 9 months ago - 2 comments
Labels: enhancement

#274 - mpDockQ/pDockQ scores seem >1 for 3-protein complexes

Issue - State: closed - Opened by niradsp 9 months ago - 6 comments

#273 - fixed the sorting and now it sorts numerically

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

#272 - IndexError when predicting monomers with more than 3 recycles

Issue - State: closed - Opened by maurerv 9 months ago - 3 comments

#271 - Update example_1.md

Pull Request - State: closed - Opened by DimaMolod 9 months ago
Labels: documentation

#270 - Fix mmseqs issue60 issue176 issue177

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

#268 - Update truemultimer

Pull Request - State: closed - Opened by dingquanyu 9 months ago - 1 comment

#267 - create_individual_features.py: command not found

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

#266 - Create feats merged

Pull Request - State: closed - Opened by DimaMolod 9 months ago - 2 comments

#265 - convert_to_modelcif on top directory scenario

Issue - State: closed - Opened by jkosinski 9 months ago - 2 comments
Labels: enhancement

#264 - check_predict_structure.py not passing

Issue - State: closed - Opened by jkosinski 10 months ago - 1 comment
Labels: bug

#263 - Fix versions in example 1

Pull Request - State: closed - Opened by jkosinski 10 months ago - 1 comment

#262 - Crashing because of missing stereo_chemical_props.txt

Issue - State: closed - Opened by jkosinski 10 months ago
Labels: help wanted

#261 - Update example_1.md

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

#260 - Update Developing.md

Pull Request - State: closed - Opened by jkosinski 10 months ago - 3 comments

#259 - Is this file committed to test/ by mistake?

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

#256 - Generate Distogram and MSA coverage

Issue - State: open - Opened by Qrouger 10 months ago - 7 comments

#255 - How to run multimer_jobs.py with relaxed model option?

Issue - State: closed - Opened by herman-einstein 10 months ago - 1 comment

#254 - Autormsd

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

#253 - CPU part silently failing for a particular protein

Issue - State: closed - Opened by sroet 10 months ago - 2 comments

#252 - Link to an existing AlphaFold2 installation

Issue - State: closed - Opened by nmarounina 10 months ago - 2 comments

#251 - May I know how to execute run_multimer_jobs.py with CPU

Issue - State: closed - Opened by herman-einstein 10 months ago - 8 comments

#250 - No module named 'alphafold.version'

Issue - State: closed - Opened by cmwilson252 10 months ago - 3 comments

#247 - Make fasta parser work with default uniprot descriptions

Issue - State: closed - Opened by DimaMolod 10 months ago - 1 comment
Labels: bug

#246 - Update example_3.md

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

#245 - maxres and maxfilt flags not working

Issue - State: closed - Opened by BelminLeiden 10 months ago - 3 comments

#244 - Modelcif conversion

Pull Request - State: closed - Opened by bienchen 11 months ago - 1 comment
Labels: enhancement

#243 - alpha_analysis_jax_0.4.sif python issue

Issue - State: closed - Opened by BobCoelingh 11 months ago - 9 comments

#242 - Merge newest AlphaFold

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

#241 - allow_resume can be very slow

Issue - State: open - Opened by jkosinski 11 months ago

#240 - modeling json with flags/versions

Pull Request - State: closed - Opened by DimaMolod 11 months ago

#239 - Modelcif

Pull Request - State: closed - Opened by DimaMolod 11 months ago - 1 comment

#238 - update to main

Pull Request - State: closed - Opened by DimaMolod 11 months ago

#237 - fail to initialise cuda backend

Issue - State: closed - Opened by grandrea 11 months ago - 3 comments

#236 - fixed links, typos, md formatting

Pull Request - State: closed - Opened by quantixed 11 months ago - 1 comment

#235 - Add option of using mmseqs2 template search instead of hmmer for template search

Issue - State: closed - Opened by jkosinski 11 months ago - 1 comment
Labels: enhancement

#234 - Fresh install fails SCOPData from Bio.Data import

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

#233 - Error for specific proteins

Issue - State: closed - Opened by roderickslieker 11 months ago - 31 comments
Labels: help wanted

#232 - create features scripts crash in the newest version

Issue - State: closed - Opened by aokosinska 11 months ago - 3 comments
Labels: bug

#231 - create_individual_features_with_templates.py doesn't work with the latest Biopython

Issue - State: closed - Opened by aokosinska 11 months ago
Labels: documentation