I believe the key might be to pass parameters to the file loader to
specify WHICH alt locations you want to load --- you could load as
many as you like; they would come in (in a sense) like vibrations, and
you would not have to pull in the whole file. In the prototype I have
implemented
load "filename" 4
The four means "just load the fourth model". It works great. The idea
is that one might have, say, a collection of crystal structures. One
is only going to look at one at a time, so this allows selective (and
much speedier, because of all the necessary symmetry handling) file
loading.
I could imagine this becoming something like:
load "filename" 4,7,8,12
(commas ignored; just for readability here)
which would say, "load three models from "filename" -- the 4th, the
7th, ....
Just a possibility.
Bob
Miguel wrote:
Miguel,
Q: Are these distinct atoms in the same 'model' or in
different 'models' ?
They are real and distinct atoms in the same model, which is a big
downside of PyMOL's approach.
OK
count_atoms, for instance, will be
increased...even though that isn't right from a conceptual standpoint. Of
course, the atom count could probably be weighted by the occupancies, and
in theory occupancies should sum to 1.0, but...well, you get the idea --
it is a bit of a mess.
Understood.
Some time ago I did some prototyping where I put all of the altLoc atoms
in the same model. One of the first things that I saw was that the
'autobond' code that builds connectivity just fell apart. Places where
there altLoc atoms just turned into a knot of spaghetti.
This is one of the things that made me think that it was necessary to
build separate models. But, the number of distinct models quickly gets too
large.
Miguel
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Professor of Chemistry, St. Olaf College
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