RosettaCommons/PyRosetta.notebooks

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Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Stars: 709
Forks: 173
Open beginner issues: 0
Indexed issues: 29
Avg merge: 5m
Merged PRs (30d): 2

Dominant language: Jupyter Notebook
License: MIT
Last GitHub push: Sep 14, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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29 open issues indexed

Problem with lowres docking script hanging after a couple of decoys Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

RosettaCommons/PyRosetta.notebooks#116 · 1 comment · Opened Jul 2, 2026
Notebook 3.02 Typo Open

Difficulty 1/5 Under an hour Newbie friendliness 78/100

RosettaCommons/PyRosetta.notebooks#113 · Opened Feb 5, 2026
# Critical Bug: Segmentation Fault in MutateResidue on PyRosetta M1 (ARM) Build Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

RosettaCommons/PyRosetta.notebooks#111 · Opened Dec 4, 2025
Kernel Die in FastRelax Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

RosettaCommons/PyRosetta.notebooks#110 · 2 comments · Opened Sep 2, 2025
ncAA-protein mutageneis scoring Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/PyRosetta.notebooks#109 · Opened Aug 24, 2025
Linking Pymol with Pyrosetta on windows 10 using UBUNTU Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

RosettaCommons/PyRosetta.notebooks#108 · 4 comments · Opened Jun 30, 2025
what is the academic email Open

Difficulty 2/5 1-3 hours Newbie friendliness 20/100

RosettaCommons/PyRosetta.notebooks#107 · 1 comment · Opened Jun 14, 2025
Declare_chemical_bond between 2 SG atoms on the sidechain of 2 Cys residues Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/PyRosetta.notebooks#106 · 4 comments · Opened Mar 13, 2025
Conda release of 2024.42+release.3366cf78a3-py311_0 requires GLIBC_2.27 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

RosettaCommons/PyRosetta.notebooks#105 · Opened Dec 25, 2024
An error in GALigandDock: ERROR: error! pharmacophore docking requires reference_pool to be as 'INPUT'! Open

Difficulty 4/5 3-5 days Newbie friendliness 22/100

RosettaCommons/PyRosetta.notebooks#102 · Opened Jun 17, 2024
Inquiring regarding DNA model tutorial Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/PyRosetta.notebooks#101 · 2 reactions · Opened Jun 8, 2024
class RNA_DeNovoProtocolMover.de_novo_setup_from_command_line() or apply() can't run normally Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/PyRosetta.notebooks#100 · 1 comment · 2 reactions · Opened May 3, 2024
Request to add tutorial for building cyclic peptides Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

RosettaCommons/PyRosetta.notebooks#99 · 6 comments · Opened Apr 16, 2024
Segmentation fault when importing ESMFold and Tokenizers from transformers along with Pyrosetta Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

RosettaCommons/PyRosetta.notebooks#97 · Opened Jan 31, 2024
Why the mutation can not be executed thoroughly? Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

RosettaCommons/PyRosetta.notebooks#93 · 2 comments · Opened Sep 2, 2023
ERROR/warning when read pdb files Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

RosettaCommons/PyRosetta.notebooks#91 · 1 comment · Opened Aug 23, 2023
Preparing Protein, cutoff of 1.5 REU, convert the REU to kcal/mol? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/PyRosetta.notebooks#90 · Opened Jun 12, 2023
How can I execute this command in pyrosetta? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/PyRosetta.notebooks#88 · 3 comments · Opened Jun 7, 2023
Running PyRosetta on Google Colab Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/PyRosetta.notebooks#86 · 2 comments · Opened Apr 17, 2023
Unable to access the software, 401 unauthorized Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

RosettaCommons/PyRosetta.notebooks#85 · 1 comment · Opened Jan 22, 2023
add acetylated N-terminus using pyrosetta Open

Difficulty 3/5 1-2 days Newbie friendliness 20/100

RosettaCommons/PyRosetta.notebooks#83 · Opened Sep 16, 2022
IndexError in Notebook 06.07 - Denovo Protein Design Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

RosettaCommons/PyRosetta.notebooks#79 · 2 comments · Opened Apr 25, 2022
How to customize the scoring function? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/PyRosetta.notebooks#78 · Opened Apr 10, 2022
Access data of the movements performed and if they were rejected or no Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

RosettaCommons/PyRosetta.notebooks#75 · Opened Jan 5, 2022
please, give example of using snugdock from pyrosetta Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

RosettaCommons/PyRosetta.notebooks#74 · 1 reaction · Opened Dec 22, 2021
Missing sections Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

RosettaCommons/PyRosetta.notebooks#71 · Opened Jul 17, 2021
Is there a way to solve the python version conflict between PyRosetta (Python 3.6) and Colab (Python 3.7) Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

RosettaCommons/PyRosetta.notebooks#63 · 2 comments · Opened Mar 2, 2021
15.1 failing in master Open

RosettaCommons/PyRosetta.notebooks#60 · 1 assignee · Opened Feb 16, 2021
Make readme.md more like a title page Open

paper

RosettaCommons/PyRosetta.notebooks#31 · 1 assignee · Opened Jan 8, 2020

RosettaCommons/PyRosetta.notebooks

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