With Tim Driscoll's support I have changed the implementation of many
important predefined sets within Jmol.
Most predefined sets related to protein & nucleic were affected. We
believe that these are much more useful definitions.
Please be on the lookout for bugs.
Oh yes ... this work had a beneficial side-effect in the area of
nucleotide graphic shapes. I encourage you to load up some DNA/RNA, in
.cif or .pdb format, and try:
cpk off; wireframe off; cartoons
Miguel
Detail
------
The definitions of the following were affected:
protein - now includes modified residues
backbone/mainchain - for protein now includes OXT & appropriate H
sidechain
nucleic,dna,rna,purine,pyrimidine,a,c,g,t,i,u,tu ...
... all have new robust definitions provided by Tim.
Tim wrote:
> attached (pdf) is a rubric we can use to separate
> out the various nucleotide predefined sets.
Tim,
Your document was extremely helpful for me. I added it to cvs so that we
don't lose it.
Over the weekend I rewrote all the Group support code. Previously I told
you that this code was a disaster ... the infrastructure it is now in much
better shape.
I think the class hierarchy underneath Group is now quite solid:
Group
Monomer
AlphaMonomer
AminoMonomer
NucleicMonomer
Chain
Polymer
AlphaPolymer
AminoPolymer
NucleicPolymer
In addition, the mechanism for detecting groups is now very good. I think
we will be in a good position to add carbohydrate and lipid support at
some point down the road.
Miguel
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