Skip to content
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

Jump to bottom

Residue.chi1_angle() selection is incomplete #2044

Closed
orbeckst opened this issue Aug 12, 2018 · 0 comments · Fixed by #3241
Closed

Residue.chi1_angle() selection is incomplete #2044

orbeckst opened this issue Aug 12, 2018 · 0 comments · Fixed by #3241
Labels
Component-Core Component-Selections defect Difficulty-easy Format-PDB GSOC Starter

Comments

@orbeckst
Copy link
Member

orbeckst commented Aug 12, 2018 •
edited
Loading

Expected behavior

Residue.chi1_angle()

mdanalysis/package/MDAnalysis/core/topologyattrs.py

Line 614 in 388346d

def chi1_selection(residue):
should find all chi1 angles for all residues for standard PDB files from the Protein Databank.

Actual behavior

@hfmull noticed in https://github.com/MDAnalysis/mdanalysis/pull/2033/files#r208769338 that the standard selection is incomplete. He implemented a custom selection in the new analysis.dihedrals.Janin class.

Code to reproduce the behavior
Need example file.

See #3238 for example.

Currently version of MDAnalysis

develop 0.18.1-dev
@orbeckst orbeckst mentioned this issue Aug 12, 2018
Merged
3 tasks
@orbeckst orbeckst mentioned this issue Apr 23, 2021
Closed
@lilyminium lilyminium mentioned this issue Apr 23, 2021
Merged
4 tasks
orbeckst pushed a commit that referenced this issue Apr 28, 2021
@lilyminium
Patch chi1_sel to match all gamma atoms (#3241)
8bc6ca3 
* Fixes #2044
* chi1 selection now follows IUPAC 1970 convention for the gamma heavy atom (IUPAC-IUB Commission 1969 Draft (doi: 10.1021/bi00820a001)) for standard protein amino acids
* added tests
* add warning to chi1_selection() docs (Janin analysis class uses stricter convention from the Janin 1978 paper)
* update CHANGELOG
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
Component-Core Component-Selections defect Difficulty-easy Format-PDB GSOC Starter
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Patch chi1_sel to match all gamma atoms lilyminium/mdanalysis
1 participant
@orbeckst