From: Miguel <mi...@jm...> - 2004-12-19 16:23:57
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Egon wrote: >> > Egon wrote: >> > > Ok, what AtomIterator method should return the PDB atom names? >> > >> > JmolAdapter.AtomIterator.getAtomName() >> >> Ok, working on it. > > That was too easy... :) Good. Things generally work better when they are easy ;-) > The PDBReader now stores the PDB atomtype CA etc, as > AtomType.getAtomTypeName(), and Jmol's CdkJmolAdapter uses that to retu= rn > with getAtomName()... > > Trace, backbone, cartoons and ribbons work now. Fantastic=21 > What's next? :) (patches being commited...) Don't know ... let's see ... try it out on some DNA ... samples/pdb/1D68.pdb Try 'cartoons' and make sure that the nucleotide bases are being recognized properly. Try an alpha-carbon-only protein ... samples/pdb/1ALM.pdb Make sure that you are returning the 'chain' character correctly. using something that has more than 1 chain ... samples/pdb/1A00.pdb, 'color chain' If you have implemented all the things in the JmolAdapter.AtomIterator, then it (hopefully) should just work. Miguel |