so true! Thanks, Eric. I see the documentation is wrong for "protein" and
missing for "nucleic" and several other not-so-obvious definitions, such as
dna, rna, purine, and pyrimidine. I have updated the documentation at
http://chemapps.stolaf.edu/jmol/docs/?&fullmanual=1&ver=14.4#atomexpressions
and have made some adjustments in Jmol as well:
Jmol.___JmolVersion="14.3.16_2015.08.23"
FEATURE CHANGE: Definitions of dna, rna, purine, and pyrimidine were
ambiguous and
not particularly viable for group fragments. This is much
clearer
now: Fragments and P-only and N-only monomers are
identified by
name only:
// These masks are only used for P-only and N-only polymers
// or cases where there are so few atoms that a monomer's type
// cannot be determined by checking actual atoms and connections.
// They are used for NucleicMonomer or AminoMonomer classes only as
// a last resort.
//
// I A G
// purine: 100101 = 0x25
// UT C
// pyrimidine: 011010 = 0x1A
//
// +IUTACGDIUTACG IUTACG
// rna: 110000 000000 110111 = 0x30037
// +IUTACGDIUTACG IUTACG
// dna: 001111 111111 001000 = 0x0FFC8
bug fix: set cartoonLadders with phosphorus-only polymers crashes Jmol
bug fix: protein and nucleic are not set properly for non-monomer groups
(Eric Martz)
-- broken in Jmol 14.3.11 (12/13/2014)
-- general definition of protein is from having CA, C, and N. But there
are situations where we know it is protein from its group name
(ALA,LEU..)
despite the fact that it is just one atom. Same for nucleic.
-- note that non-canonical (HETERO) amino acids or nucleic bases that do
not have
the requisite atoms to identify them as such will still not test
positive for
"protein" or "nucleic".
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