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Document for selection with canonical attributes #170

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yuxuanzhuang opened this issue Sep 23, 2021 · 1 comment
Open

Document for selection with canonical attributes #170

yuxuanzhuang opened this issue Sep 23, 2021 · 1 comment

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@yuxuanzhuang
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Is your feature request related to a problem? Please describe.

I'm always frustrated when I try to figure out what the canonical attributes syntax is for residues. It is not mentioned in the userguide but only (I think?) in the documents. Besides, it is not directly listed as a keyword in the document but on a separate page.

Describe the solution you'd like

  • Add similar descriptions of how to use canonical attributes to select residues/chains/... in the userguide.
  • It's a long paragraph when talking about selecting with topology attribute and people (I) tend to omit. It would be great to mention some of the important ones, e.g. resindex, as an example directly on the same page.
  • Maybe add a section on selection syntax differences between different software so people migrate from another environment can get easily accustomed to MDAnalysis.
e.g. 
for PDB files
in VMD: residue 10 \ resid 10
in MDAnalysis: resindex 10 (or 9?) \ resid 10
in gmx_select: ...
...
@IAlibay
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IAlibay commented Sep 23, 2021

Sounds like a good idea (unless I'm forgetting some existing text)!

Anything to make selections clearer would be great - could possibly be an opportunity to add things related to @lilyminium's improvements to the flexibility of selections (unless it's already somewhere?)

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