One of the recent features is the “template tool” which helps to assemble metal complexes and functional groups.
I’m building up a bigger library of ligands, but this also requires preview images. The auto-generation script (which uses RDKit) is … not great (to say the least) at handling multi-dentate ligands.
I could use some help re-drawing some of the following, (And if you have ideas for other common ligands, please add some comments below.)
Yes. While I’m open to input, I showed a variety of examples to both colleagues and students here and showing the bonds to the metal site were clearly preferred. Ideally, I’d like to keep the depiction of the phenyl rings as well.
The unloaded triphos ligands, for example, dont’ show much in the way of “how does this ligand wrap a metal.”
Thanks for the cyclam. For whatever reason, I hadn’t tried the SMILES in ChemDraw and it’s generating a reasonable image:
Biased because being used to read “Ph” as “phenyl group”, a triphos formula like the one below were “iconic enough” for me (I attach the files in the archive attached) – both with Irfan View scaling to 20% on a non-retina display, as well as an icon in file browser Thunar, with about 60 by 60 pixels for the illustration it self (about 1.6 cm or approx 0.5").
It is not the red of red nose day… the first association I got with cyclam redrawn by you.
triphos.tar.gz (22.0 KB)
Because of the shortened US American version for the British original. But re the icons for Avogadro: if the drawing is easy discernible at distance/small dimension, then the icon is good.
For future reference, all the geometries and images are here - pull requests and comments are most welcome:
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