Discrete grid for building structures

I’m not sure it’s a bug, but I just wanted to discuss a difference between Avo1 and Avo2:



Avo 2:


Notice how it seems like Avo1 is using a continuous grid for possible placements of an atom while Avo2 uses a discrete one. I was wondering whether it’s intentional and what’s the rationale for that.

With discrete grid it somewhat feels less pleasant, as if the build tool is lagging, although that may not be the most important consideration.

This seems to be a newer thing. I’m not sure if it’s a slight rendering hiccup because of the shadow rendering?

Ages ago, I tried out a “snap to grid” option for drawing and for the reasons you mention, it wasn’t well received.

The easy way to test is to compare against 1.97, which doesn’t have the real-time shadows.

1 Like

Actually, I just tried a few older versions. Seems as if it happened in the 1.94 → 1.95 release.

I’ll check some profiling to see where it’s spending time.

1 Like

Sorry for not mentioning it earlier, this is all from 1.97 pre-shaders (I thought they could be the cause, but no)

The example shown is how to build ethane when starting with methane. If one spent some time building molecule models with a model kit, and would add an other single bond to the next carbon (i.e, ethane → propane), the bend in the line C-C-C, or the zig-zag in C-C-C-C butane is not too surprising. Actually, it helps to close the loop when constructing e.g., cyclopentane and cyclohexane from scratch, without assistance of templates.

By the way, the monodentate derived from ammonia is amine; for some reason, the GUI of the test release misspells it as ammine. Not only that this deviates from IUPAC (as a typo), it would sound differently (length and stress of the syllables) when spoken,

I think it was just an example that the rendering is hiccuping as if it’s only allowing certain bond lengths and angles. (No, there seems to be a rendering speed issue that I’m looking into. One bug was that icons were loaded many, many times.)

Well if that’s the IUPAC recommendation, it’s newer than when I learned ligand names. And double-checking now … it’s the correct spelling for coordination compounds:

Okay, found the cause - git bisect to the rescue. Thanks for the feedback, along the way I found several other optimizations.

Basically, a small logic error crept into the editor code. (Ignore the preview on the forum - I found the full solution this morning.)

1 Like

@ghutchis you are right; I erred.

For me, it was worth to consult the Red Book (edition 2005) again to recognize

  • amine (one m) is to be used in 1) the additive nomenclature of complexes for neutral organic ligands carrying at least one carbon atom or for hydroxylamine (IR- Or – in parlance of Table IX – where it is meant as ligand and “parent name for certain organic derivatives”.

    The substitutive nomenclature (IR-6.3.2) equally knows amine – NH2 units as a bridge as in example 4 diboran(6)-µ-amine. But these are not Werner-like complexes with a transition metal in the center.

  • by the Red Book, ammine (with two m) describes uncharged ammonia binding to a metal, introduced by rule IR-7.1.3 representing ligands in additive names.

So indeed, I erred taking a perspective too much influenced by organic chemistry; to drop the second “m” thus indeed is incorrect. Yet (still?) this is encountered as mentioned in the French edition of the Ammine article

il est par ailleurs fréquent de rencontrer les deux formes dans la littérature, souvent avec un seul « m » même en l’absence de chaîne carbonée.

which translates to

(both forms [of writing, one or two “m”] are frequently found in the literature, often only with only one “m” regardless of the absence of a carbon chain.

for French, yet equally matching occasional observation in English. E.g., the name for “Pentaamine(dinitrogen)ruthenium(II)” (center example on Metal-Ammine Complex) is not correct. Then I came to notice the second and fourth example of the same page do not follow IR- number of ligands in a coordination entity defining the corresponding prefixes either; this closes with “There is no elision of vowels or use of a hyphen, e.g. in tetraammine [two “a” and two “m”] and similar names.” In other words, “Pentamminerhodium chloride” should be replaced by “Pentaamminerhodium chloride”, and “Hexamminecobalt(III) chloride” by “Hexaamminecobalt(III) chloride”.

In this regard, I now going to read (machine generated?) entries, e.g., on ChemIDplus, tab Names & Synonyms equally more critical e.g.,

Potassium aminetrichloroplatinate(II)
Platinum tetramine dichloride
Hexaaminecobalt trichloride
2-(5-Cyanotetrazolato) pentaamine cobalt III perchlorate

Thank you a lot!

[1] Red Book - IUPAC | International Union of Pure and Applied Chemistry
[2] Ammine — Wikipédia