Hi James, There's something very strange going on here with PyMol.
On Oct 25, 2013, at 1:09 PM, James Davidson wrote: > I can't see any double-bonds rendered in PyMOL: > CONECT 3 4 4 10 Here atom 3 has two bonds to atom 4. Why isn't it displayed double? > This PDB *will* render double bonds in PyMOL. > CONECT 3 4 4 As expected. > (and, again, I also see double bonds in PyMOL). > CONECT 3 2 4 10 No explicit double bond. Where is the double bond coming from? I'd expect two of the above cases to show double bonds, and one to only have single bonds. What is confusing is that which is which doesn't make any sense. > Can you (or Greg) post a list of what the current input flavors do? Currently the reader only has a single flavor... flavor & 1 : Read alternate locations, XPLOR/NMR pseudo atoms, and PDB dummy residues. By default the PDB file reader only returns atoms with alternate locations fields of space, 'A' or '1'. It also ignores atoms with co-ordinates 9999.000, 9999.000, 9999.000 that appear in XPLOR output for leaving group atoms in covalently bonded ligands. Likewise, atoms with atomic symbol " Q" which are typically dummy atoms used as refinement constraints in NMR refinement. If the flavor parameter has the value 1, all these pseudo-atoms are read into the RDKit::ROMol, but clearly their semantics isn't understood by the rest of the toolkit. Valences will be incorrect, and a protein with multiple alternate sidechain conformations for some will likely fail sanitization. I hope this helps. Roger -- Roger Sayle, Ph.D. CEO and founder NextMove Software Limited Registered in England No. 07588305 Registered Office: Innovation Centre (Unit 23), Cambridge Science Park, Cambridge CB4 0EY ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
