Skip to content

Issues: openmm/pdbfixer

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

45 Open 156 Closed
45 Open 156 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Remove use of cgi module
#318 opened Nov 10, 2024 by peastman
PDBFixer - in some cases added residues have amides with non-trans OCNH stereochemistry bug
#307 opened Sep 30, 2024 by ivanicj
1
14
Weird coordinates and unable to add Hydrogens upon adding tyrosines
#304 opened Aug 20, 2024 by sukritsingh
5
Should PDBFixer write out SEQRES entries if provided in the input?
#293 opened Jun 6, 2024 by sukritsingh
9
The repair of two ends of peptide didn't return the desired result
#283 opened Dec 6, 2023 by bdx114514
PDBFixer cannot handle nucleic acids with residue name N
#281 opened Nov 14, 2023 by jamesmkrieger
5
Do we have method to mutate the iCode-containing residue? enhancement
#280 opened Oct 11, 2023 by locitran
2
pypi version
#254 opened Oct 21, 2022 by Pantelispanka
13
PDBs from RCSB failed to reconstruct
#219 opened Mar 30, 2021 by slawek111
7
Charges lost on ASP and GLU residues
#210 opened Oct 12, 2020 by tdudgeon
1
How to select a single position for atoms with multiple alternate positions listed enhancement
#205 opened Aug 13, 2020 by ghost
3
Residue number strange behavior
#201 opened Apr 16, 2020 by MauriceKarrenbrock
2
List of fixes for failing test cases
#199 opened Mar 5, 2020 by zhang-ivy
2
Wrong placement of added hydrogens. enhancement
#179 opened Oct 16, 2018 by niko97320
9
Non-reproducible behaviour of addMissingAtoms
#176 opened Oct 3, 2018 by JoaoRodrigues
pdbfixer is mislabeling built residues with negative res IDs
#175 opened Oct 3, 2018 by nitroamos
5
More rigorous implementation of findMissingResidues needed (e.g., doesn't work for antibodies)
#170 opened Jun 4, 2018 by nitroamos
13
Add Zenodo DOI?
#166 opened May 6, 2018 by jchodera
Exception: Particle coordinate is nan in addMembrane
#163 opened Apr 17, 2018 by nitroamos
6
Getting version? bug
#146 opened Jan 24, 2017 by davidlmobley
4
N-terminal residue added with wrong chirality and/or a cis-peptide bond
#145 opened Jan 10, 2017 by rafwiewiora
29
addMissingHydrogens() fails under Windows
#142 opened Nov 1, 2016 by jepdavidson
3
findMissingResidues() does not work on files that have been through pdbfixer already
#138 opened Jul 20, 2016 by rafwiewiora
2
Citing pdbfixer
#137 opened Jul 20, 2016 by jchodera
2
Enable nightly builds
#129 opened Apr 10, 2016 by jchodera
2
ProTip! What’s not been updated in a month: updated:<2024-11-29.