Sara,
You can (always) load just the first configuration of a model that has two
alternative configurations using the "conf" filter:
load =1trz filter "conf 1"
load =1trz filter "conf 2"
Like that. Then only those atoms that have no alternative atom location or
the first/second alternative locations will be loaded (A/B in this case).
There is some ambiguity in terms of alternative atom locations and what they
mean in PDB files. Sometimes they are just two different options for where
the atoms are; sometimes they are completely different groups, like ARG and
LYS. The A and B refer to two options within a given group. There could be
tens or hundreds of different possible models if there are alternative atom
positions marked for different groups. Jmol doesn't attempt to sort all that
out, and instead just (a) loads all the atoms if you don't specify a filter,
and (b) lets you do a quick check of one overall set of positions relative
to another with the "configuration" business.
If you load all the atoms, then you can still display a specific
configuration:
load =1trz
display configuration=1
display configuration=2
like that.
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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