Comment - FBXL Lotide

Comment on Need Feedback - Changing Bond Lengths - Discoverability

ghutchis@discuss.avogadro.cc ⁨2⁩ ⁨weeks⁩ ago

Well, for now I’m going with that, since everything else is based on changing bond lengths.

draft edit panel in the measure tool

draft edit panel in the measure tool1354×316 61.1 KB

So it’s fairly easy to move the two oxygen atoms relative to each other to a specific distance.

Thoughts? Suggestions? Complaints?

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Thomas@discuss.avogadro.cc ⁨2⁩ ⁨weeks⁩ ago
Is a manual setup of bond lengths and angles in addition to a readout a frequent / typical need in computational chemistry?

So far, I did not consider to miss such a dial next to the readout, especially because Avo2 updates the values if atoms are moved / groups swing around a bond with the mouse tool, etc.
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- ghutchis@discuss.avogadro.cc ⁨2⁩ ⁨weeks⁩ ago
  Image Thomas:
  
  So far, I did not consider to miss such a dial next to the readout, especially because Avo2 updates the values if atoms are moved / groups swing around a bond with the mouse tool, etc.
  
  I think there are two common uses:
  
  setting a specific value of a distance, angle, dihedral as part of a scan (e.g., how does the energy change around this torsion)
  
  setting up the geometry of a non-bonded cluster (e.g., water dimer as indicated above)
  
  In general, I’ve used other methods. But it came up a few times in the survey results and it seems other methods weren’t very discoverable. So I want to improve some task-based documentation as well as discoverability. (The z-matrix editor will probably also help.)
  
  Image Thomas:
  
  a) this could be complemented by dials of the three axes (similar to e.g., inkscape "rotate this selected shape by x degrees in in clock/anticlockwise direction), or b) right away with an input for the Eulerian rotation matrix.
  
  There’s probably a good way to have this in the manipulate tool (or a new tool). Several people have asked for ways to rotate a Cp ring around the axis.
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- Thomas@discuss.avogadro.cc ⁨2⁩ ⁨weeks⁩ ago
  Re the relative orientation of two sets of atoms: hjkl might be a bit coarse,* because naturally it runs in increments. If this were to coarse (additional input by other users welcome), perhaps a) this could be complemented by dials of the three axes (similar to e.g., inkscape "rotate this selected shape by x degrees in in clock/anticlockwise direction), or b) right away with an input for the Eulerian rotation matrix. I think if not a), version b) could be “too much effort” for Avogadro2.
  
  * Of course not to be called vim tool. There are times vim is more suitable, and other times Emacs (e.g., orgmode) for different purposes.
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