A few days ago, Miguel asked whether altLoc's were correlated (e.g. all A's
go with all other A's as a "model") or not (each A vs. B altLoc is
independent of the other A's and B's).
Scott Garman, a crystallographer, kindly sent some clarification which I
will paraphrase as follows. Experimentally, altLoc's are assigned when the
electron density supports two distinct positions for the same atoms (in
different copies of the molecule in the crystal). (In unusual cases there
could be evidence for three or more positions, but often the electron
density would get too blurred to be sure beyond two.)
If only side-chain atoms, (CB = carbon beta, CG = carbon gamma, NH =
nitrogen eta, etc.) have altLoc's, each side chain's A altLoc positions are
independent (uncorrelated) with the A altLoc's of other side chains.
If both side-chain and main chain (CA = carbon alpha, N = main chain
nitrogen, C = main chain carbon) atoms have altLoc for a consecutive run of
amino acids, then they are alternate positions for the entire run, so all
the A altLoc's are one local conformation, and all the B altLoc's are another.
I say "local" because farther down the chain could be another run of
altLoc's A and B, but the second run of A need not go with the first. The
first run could be in conformation altLoc A, while the second is in B in
the same molecule.
So the bottom line is that altLoc's can be uncorrelated or locally
correlated in a consecutive run, but still uncorrelated between different runs.
I don't think Jmol needs to have any intelligence built-in about this,
beyond that the implementation should allow for the absence of correlation
between different A's or runs of A's -- it certainly should not assume that
all altLoc A's are "one model".
-Eric
----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz
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