In working with CIFs we have a need to manage files with several types of coordinates:
2D - chemical structural diagram - NOT related to 3D diagram
3D - atom positions
5D a file with both
8D as above but also with fractional coordinates.
We need to be able to display (not necessarily edit) these combinations. The display of 2D and 3D coordinates is fundamentally different. A 2D display should NOT be rotatable (this is very dangerous) and normally includes character symbols rather than balls for the atoms. It also includes formal charges and isotopes.
What should/does Jmol do when getting different files? At present I think it does the following:
- if xFract is present, sue those coordinates and draw the unite cell
- else if x3 draw a 3D molecule
- else if 2D draw a 2d "rotatable" molecule.
The latter should not happen. 2D molecules are flat by definition and are not 3D objects. Rotating them is actually very dangerous as people think they are real 3D objects.
Ideally I think that Jmol should provide separate 3D and 2D windows, the latter perhaps based on a "Jchempaint applet". Egon and we will be meeting soon and can discuss this. At present I am using Marvin for input and display of 2D structures though I would obviously prefer Jchempaint because we can develop an event model, etc. I would prefer not to have to develop a 2D renderer independently of Jchempaint but there is currently a fairly urgent need as CML is now starting to spread in a number of places where this is required.
Best
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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