Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / rosettacommons/rfdesign issues and pull requests

#57 - error while running Rifdock protocol

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

#57 - error while running Rifdock protocol

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

#56 - Can not install jaxlib==0.3.24 under cuda 12 environment

Issue - State: open - Opened by erwusht 12 months ago - 1 comment

#56 - Can not install jaxlib==0.3.24 under cuda 12 environment

Issue - State: open - Opened by erwusht 12 months ago - 1 comment

#55 - Not found /software/rosetta/DAlphaBall.gcc

Issue - State: open - Opened by double-vin over 1 year ago - 3 comments

#55 - Not found /software/rosetta/DAlphaBall.gcc

Issue - State: open - Opened by double-vin over 1 year ago - 3 comments

#53 - Type Error with af2_interface_metrics.py

Issue - State: open - Opened by aravinda1879 over 1 year ago - 3 comments

#53 - Type Error with af2_interface_metrics.py

Issue - State: open - Opened by aravinda1879 over 1 year ago - 3 comments

#52 - Information on split_folder command

Issue - State: open - Opened by aravinda1879 over 1 year ago - 2 comments

#52 - Information on split_folder command

Issue - State: open - Opened by aravinda1879 over 1 year ago - 2 comments

#51 - no PDBs output/NameError: name 'aa_util' is not defined

Issue - State: open - Opened by morin-andrew over 1 year ago - 3 comments

#51 - no PDBs output/NameError: name 'aa_util' is not defined

Issue - State: open - Opened by morin-andrew over 1 year ago - 3 comments

#50 - AF2_metrics jax error

Issue - State: open - Opened by JonathanEAsh over 1 year ago

#50 - AF2_metrics jax error

Issue - State: open - Opened by JonathanEAsh over 1 year ago

#49 - Error in running hallucination

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

#49 - Error in running hallucination

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

#48 - Error while running af2_interface_metrics.py

Issue - State: open - Opened by leejy9548 over 1 year ago - 3 comments

#48 - Error while running af2_interface_metrics.py

Issue - State: open - Opened by leejy9548 over 1 year ago - 3 comments

#46 - fix: exit with code 0 when successfull

Pull Request - State: open - Opened by karvla almost 2 years ago

#46 - fix: exit with code 0 when successfull

Pull Request - State: open - Opened by karvla almost 2 years ago

#45 - Af2_metrics error

Issue - State: closed - Opened by Lyang556 almost 2 years ago

#45 - Af2_metrics error

Issue - State: closed - Opened by Lyang556 almost 2 years ago

#44 - RuntimeError: CUDA out of memory.

Issue - State: open - Opened by slives-lab almost 2 years ago

#44 - RuntimeError: CUDA out of memory.

Issue - State: open - Opened by slives-lab almost 2 years ago

#43 - Alphafold2 Monomer Metrics

Pull Request - State: closed - Opened by mdamgaard-biolib almost 2 years ago - 1 comment

#43 - Alphafold2 Monomer Metrics

Pull Request - State: closed - Opened by mdamgaard-biolib almost 2 years ago - 1 comment

#42 - A possible misleading comment.

Issue - State: open - Opened by zackmawaldi almost 2 years ago - 1 comment

#42 - A possible misleading comment.

Issue - State: open - Opened by zackmawaldi almost 2 years ago - 1 comment

#41 - psipred4 missing

Issue - State: open - Opened by jIskCoder almost 2 years ago - 1 comment

#41 - psipred4 missing

Issue - State: open - Opened by jIskCoder almost 2 years ago - 1 comment

#40 - Unclear documentation/tutorial or mistake

Issue - State: open - Opened by jaded0 almost 2 years ago

#40 - Unclear documentation/tutorial or mistake

Issue - State: open - Opened by jaded0 almost 2 years ago

#39 - DAlphaBall missing

Issue - State: open - Opened by jIskCoder almost 2 years ago - 2 comments

#39 - DAlphaBall missing

Issue - State: open - Opened by jIskCoder almost 2 years ago - 2 comments

#38 - Issue with alphafold-complex predication with initial guess of binder position

Issue - State: open - Opened by QILINY almost 2 years ago - 2 comments

#38 - Issue with alphafold-complex predication with initial guess of binder position

Issue - State: open - Opened by QILINY almost 2 years ago - 2 comments

#37 - Error while running af2_metric.py file

Issue - State: open - Opened by sssure02 about 2 years ago

#37 - Error while running af2_metric.py file

Issue - State: open - Opened by sssure02 about 2 years ago

#36 - How to mask out the amino acid in that mutation position?

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

#36 - How to mask out the amino acid in that mutation position?

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

#35 - missing compile_metrics.py file

Issue - State: open - Opened by aravinda1879 about 2 years ago - 2 comments

#35 - missing compile_metrics.py file

Issue - State: open - Opened by aravinda1879 about 2 years ago - 2 comments

#34 - SAP script

Issue - State: open - Opened by sirius777coder about 2 years ago

#34 - SAP script

Issue - State: open - Opened by sirius777coder about 2 years ago

#33 - Multiple ModuleNotFoundError

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

#33 - Multiple ModuleNotFoundError

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

#32 - Hallucination w/ receptor crashing while saving output

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

#32 - Hallucination w/ receptor crashing while saving output

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

#31 - Add Dockerfile

Pull Request - State: closed - Opened by timodonnell about 2 years ago - 4 comments

#31 - Add Dockerfile

Pull Request - State: closed - Opened by timodonnell about 2 years ago - 4 comments

#30 - Workflow for resultant inpainting models

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

#30 - Workflow for resultant inpainting models

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

#29 - Inpainting is trying to connect multiple chains

Issue - State: open - Opened by jadolfbr about 2 years ago - 8 comments

#29 - Inpainting is trying to connect multiple chains

Issue - State: open - Opened by jadolfbr about 2 years ago - 8 comments

#28 - Blank PDB?

Issue - State: open - Opened by jadolfbr about 2 years ago

#28 - Blank PDB?

Issue - State: open - Opened by jadolfbr about 2 years ago

#27 - AF2 Model Parameters Download for af2_metrics.py

Issue - State: open - Opened by Germanki about 2 years ago - 1 comment

#27 - AF2 Model Parameters Download for af2_metrics.py

Issue - State: open - Opened by Germanki about 2 years ago - 1 comment

#26 - AF2 Dependencies for af2_metrics.py

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

#26 - AF2 Dependencies for af2_metrics.py

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

#25 - AF2 metrics prediction jax error

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

#25 - AF2 metrics prediction jax error

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

#24 - predict with alphafold meet jax problem

Issue - State: open - Opened by Zhang-hn1125 about 2 years ago

#24 - predict with alphafold meet jax problem

Issue - State: open - Opened by Zhang-hn1125 about 2 years ago

#23 - Missing minterface.xml in scripts folder

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

#23 - Missing minterface.xml in scripts folder

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

#22 - ModuleNotFoundError: No module named 'tree'

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

#22 - ModuleNotFoundError: No module named 'tree'

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

#21 - Patch scripts with correct paths

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

#21 - Patch scripts with correct paths

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

#20 - May run trfold_relax.sh out of slurm possible?

Issue - State: open - Opened by DaHenz about 2 years ago - 1 comment

#20 - May run trfold_relax.sh out of slurm possible?

Issue - State: open - Opened by DaHenz about 2 years ago - 1 comment

#19 - Missing rosetta flags and xml script for relaxation in SH3 tutorial

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

#19 - Missing rosetta flags and xml script for relaxation in SH3 tutorial

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

#18 - Missing compile_metrics.py in scripts folder

Issue - State: open - Opened by BazingaOoO about 2 years ago - 1 comment

#18 - Missing compile_metrics.py in scripts folder

Issue - State: open - Opened by BazingaOoO about 2 years ago - 1 comment

#17 - Missing file in

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

#17 - Missing file in

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

#16 - Inpainting not using --receptor_chain argument

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

#16 - Inpainting not using --receptor_chain argument

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

#15 - RuntimeError: _cdist_backward requires X1 to be contiguous

Issue - State: open - Opened by philhuett over 2 years ago - 3 comments

#15 - RuntimeError: _cdist_backward requires X1 to be contiguous

Issue - State: open - Opened by philhuett over 2 years ago - 3 comments

#14 - Aborted (core dumped) when test the scripts

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

#14 - Aborted (core dumped) when test the scripts

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

#13 - Error while running af2_interface_metrics.py

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

#12 - Is there any way to provide MSA of receptor for af2_metrics.py ?

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

#11 - Update README.md

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

#10 - Unnecessary residue change when loop inpainting.

Issue - State: open - Opened by YaoYinYing over 2 years ago - 2 comments

#9 - About arguments in hallucination.py for two-chain hallucination

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

#7 - Ask about the af2 dependency under RFDesign, 'RFDesign/scripts/af2_metrics.py'

Issue - State: closed - Opened by Licko0909 over 2 years ago - 3 comments

#6 - Garbled output for inpainting

Issue - State: closed - Opened by jadolfbr over 2 years ago - 6 comments

#5 - no alphafold module in hallucination/models/

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

#4 - index out of range

Issue - State: open - Opened by yx0516 almost 3 years ago - 2 comments