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Janin analysis does not filter CYSH #2898

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orbeckst opened this issue Aug 11, 2020 · 0 comments · Fixed by #2899
Closed

Janin analysis does not filter CYSH #2898

orbeckst opened this issue Aug 11, 2020 · 0 comments · Fixed by #2899
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@orbeckst
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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

import MDAnalysis as mda; 
from MDAnalysis.tests import datafiles as data; 
from MDAnalysis.analysis import dihedrals

# 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
@orbeckst orbeckst self-assigned this Aug 11, 2020
@orbeckst orbeckst added this to the 2.0 milestone Aug 11, 2020
orbeckst added a commit that referenced this issue Aug 11, 2020
orbeckst added a commit that referenced this issue Aug 11, 2020
- 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
lilyminium pushed a commit that referenced this issue Aug 13, 2020
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)
PicoCentauri pushed a commit to PicoCentauri/mdanalysis that referenced this issue Mar 30, 2021
Fixes MDAnalysis#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)
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