Miguel wrote:
The altLocs look like this
' '
' '
'A'
'A'
'B'
'B'
' '
' '
'A'
'A'
'A'
'B'
'B'
'B'
' '
' '
and the branching looks like this
' '
' '
'A' 'B'
'A' 'B'
' '
' '
'A' 'B'
'A' 'B'
'A' 'B'
' '
' '
So, the question is ...
Q: In the general case, can the 'A' atoms from the first run/branch be
paired with the 'B' atoms from the second run/branch?
not according to the CIF documentation and examples referred to in my
previous post.
Is this a valid confomation?
' '
' '
'A'
'A'
' '
' '
'B'
'B'
'B'
' '
' '
no, until proven otherwise. There is no mechanism within the CIF
structure to allow for this.
Jmol-datafiles/pdb/1HJE.pdb
It looks like to me that it contains 6 (7?) runs with A & B branches.
Yes. 1HJE is now featured at
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm
It consists of two conformations differing primarily in the "tail".
I don't claim any expertise here. It is possible that people use this
altloc mechanism to designate independent alternatives, as Miguel has
hypothesized here. ("We don't know where these atoms are and,
independently, we also don't know where these other atoms are.") In that
case, it's still possible to show exactly what you are showing there, I
think, because with the prototype functionality you are free, for
example, to
select (1-30 and (*%,*%A)) or (31-100 and (*%,*%B))
and do your desired mix and match.
Bob
Miguel
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