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**Expected behavior**
**1. PSAnalysis.plot() produces similarly labelled plots as in PSAnalysisTutorial as the only output:**
![Screenshot 2020-01-22 at 11 49 11 PM](https://user-images.githubuser…
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@richardjgowers the notebook https://github.com/MDAnalysis/WorkshopHackathon2018/blob/master/03_Tutorial1/MDAnalysis_Workshop_Part_1.ipynb is missing. Can you please add it to the repo?
I am cleani…
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PathSimAnalysis has conda packages https://www.mdanalysis.org/PathSimAnalysis/getting_started.html#conda-mamba
Should the metadata https://mdakits.mdanalysis.org/PathSimAnalysis.html#installation-i…
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**Expected behavior**
To crash if not a water selection is given.
**Actual behavior**
It calculates with any input, not only with water molecules.
**Code to reproduce the behavior**
I'm giv…
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The code imports MDAnalysis
https://github.com/MDAnalysis/RDKitConverter-benchmark/blob/7cc1da5c934b1e1d83415b6ecdc35b109c4e2e9b/scripts/utils.py#L6-L7
Because MDAnalysis is currently licensed und…
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Hi,
I am wondering how is the interaction fps generated when there is no explicit Hs in the ligand structure file.
I used NoImplicit=False in ref_mol = plf.Molecule.from_mda(u1, NoImplicit=False) …
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~~Potentialy move streamlines to an MDAKit and out of core or remove it.~~ EDIT:
- [ ] move MDAnalysis.visualization.streamlines to MDAnalysis.analysis.streamlines
- [ ] deprecate MDAnalysis.visua…
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**Expected behavior**
DBSCAN is a clustering method that can identify outliers. I expect these outliers to be clearly indicated in some way. I also expect that outliers are treated properly in simi…
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Potentially related to MDAnalysis/mdaencore#38, but there was a request in MDAnalysis/mdanalysis#3595 to open a separate issue for the M1 mac case (using [gcc compile farm](https://cfarm.tetaneutral.n…
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## Expected behavior ##
Analysis code base is covered with test, including ENCORE.
## Actual behavior ##
Some of ENCORE's untested code appear to be dead code. See https://github.com/MDAnalys…