On May 31, 2006, at 12:05 p, Angel Herraez wrote:
so this is also a problem with the protein set as well? I'll have to
go back and see what we did here.
Maybe not. As I recall, it was something like my expectation to
select one out of two H atoms from Gly alphaC; Miguel argued that
they were backbone where I expected sidechain, or the other way
round. Anyway, I agreed on the rationale, and solved my problem with
a trick as usual (I was translating a Chime version that stopped
working the same way in Jmol).
hi Angel,
as I recall the rationale: there is no way to distinguish glycine's
"backbone" hydrogen from it's "side chain" hydrogen, either
chemically or by atom id, so Jmol calls them both backbone.
If you (and/or somebody else) go back and find the criteria being
used, I could help on compiling a doc page explaining these sets, and
put it on the Wiki for others.
inclusion in the backbone set is determined by atom id; from
JmolConstants.java:
// Terminal nuclic acid
"H5T", // 45 - 5' terminus hydrogen which replaces P + O1P + O2P
// nucleic acid backbone hydrogens
//
"1H5'", // 51 - first equivalent H on sugar 5' carbon
"2H5'", // 52 - second equivalent H on sugar 5' carbon
"H4'", // 53 - H on sugar ring 4' carbon
"H3'", // 54 - H on sugar ring 3' carbon
"1H2'", // 55 - first equivalent H on sugar ring 2' carbon
"2H2'", // 56 - second equivalent H on sugar ring 2' carbon
"2HO'", // 57 - H on sugar 2' oxygen, unique to RNA
"H1'", // 58 - H on sugar ring 1' carbon
//
"H3T", // 59 - 3' terminus hydrogen
so all of these hydrogens should be selected if you say
select nucleic and backbone
protein backbone Hs are determined in similar fashion. is it
possible that your pdb file did not use these atom identifiers?
tim
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