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The analysis.dihedral.Janin analysis removes known problematic residues. (Or fails with an intelligible error message.)
Actual behavior
When using the test TPR and XTC trajectory, the analysis fails with
ValueError: Too many or too few atoms selected. Check for missing or duplicate atoms in topology.
Code to reproduce the behavior
importMDAnalysisasmda;
fromMDAnalysis.testsimportdatafilesasdata;
fromMDAnalysis.analysisimportdihedrals# GRO works because residue 76 is "CYS"u=mda.Universe(data.GRO, data.XTC)
J=dihedrals.Janin(u.select_atoms("protein")).run()
# TPR fails because residue 76 is "CYSH"u2=mda.Universe(data.TPR, data.XTC)
J2=dihedrals.Janin(u2.select_atoms("protein")).run()
Current version of MDAnalysis
Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)") develop
Which version of Python (python -V)? 3.7
Which operating system? macOS
The text was updated successfully, but these errors were encountered:
- fix#2898
- filter CYSH (actually, CYS*)
- updated documentation with Henry Mull's Technical Report
- added Ramachandran reference
- plots have degree symbol on ticks
- updated example plots and made sure that they show what's stated in the
caption
- test added
- update CHANGELOG
Fixes#2898
- add select_protein and select_remove keywords to Janin analysis
- filter CYS* by default
- updated docs and plots
- made plots prettier (degree symbol on ticks)
FixesMDAnalysis#2898
- add select_protein and select_remove keywords to Janin analysis
- filter CYS* by default
- updated docs and plots
- made plots prettier (degree symbol on ticks)
Expected behavior
The analysis.dihedral.Janin analysis removes known problematic residues. (Or fails with an intelligible error message.)
Actual behavior
When using the test TPR and XTC trajectory, the analysis fails with
ValueError: Too many or too few atoms selected. Check for missing or duplicate atoms in topology.
Code to reproduce the behavior
Current version of MDAnalysis
python -c "import MDAnalysis as mda; print(mda.__version__)"
) developpython -V
)? 3.7The text was updated successfully, but these errors were encountered: