Peter wrote: >>Initial Comment: >>PMR points out that it would be useful to support 2D >>fisher projections. This would allow us to show >>molecules in both 2D and 3D formats. Quality of 2D >>rendering is very important. MarvinSketch has a good >>listing of standard formatting styles for fisher >>projections (explicit carbons, explicit hydrogens, only >>hydrogens connected to non-carbons, etc) > > I think you mean "2D structural diagrams". [Fischer (sic) projections are > a > (hopefully obsolescent) way of representing certain subsets of chemistry > such as sugars and amino acids]. Note that the preferred conventions are > being developed at: > http://www.angelfire.com/sc3/iupacstructures/ > which are the result of considerable recent discussion moderated by > Jonathan Brecher of CambridgeSoft.
Yes, I now understand that these are 2D projections ... and that a Fischer projection is a special type which has special interpretations for horizontal/vertical bond alignment.
Hi,
I would actually avoid the use of the word "projection" completely. They are best called "chemical structure diagrams". They are sometimes created by projecting the 3D structure onto its principal axes but this is not normally pretty and it a last resort. JCP does this if it has only 3D coords, but I would immediately use the clean function to get a "better" layout.
These diagrams may contain many other features which are not projections including abbreviated functional groups, labelling, polymer bead supports (a ball), group multipliers (polymers) , Markush ligands, etc.
.
P.
(Using google ... Fischer seemed more popular than Fisher)
Miguel
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