Bob wrote:
> Looks to me:
[snip]
> 3. a given "1" for ANY atom corresponds with a given "1" for any other
> atom. I don't see this "multiple independent run" business. Again, that
> makes no calculational sense to me at all.
That is what I used to think.
> My point is that there are certain reasonable combinations, say "1 with
> 3" and "2 with 4" that correspond to a given conformation. But "1 with
> 4" makes no sense, because the calculation only gave two conformations,
> not "all possible combinations of alternative locations."
I do not understand this.
> I could be wrong; but if I'm not, it's an easy implementation.
There has been discussion about this off-and-on for several years.
I also thought that it was easy. But then people on the mailing list said
that my understanding was incorrect.
Bob wrote:
> Miguel, are you SURE there is this "run" business?
No, I am not sure :-)
But I have gone down this path at least twice over the past few years.
Here is my understanding ...
You start with a bunch of atoms with ' ' (space) altLoc. The atom
locations are unambiguous.
Next you have a series of atoms with 'A' altLoc, followed by a series of
atoms with 'B' altLoc. These represent alternate branches in the chain.
The chain can 'fork' down one of the branches. I made up the term 'run' to
describe this. If there is a real/official term for this then I will
absolutely stop using 'run' and start using the real term.
Next you have another series of atoms with ' ' (space) altLoc. The atom
locations are unambiguous. The forks from the previous run have rejoined.
Next you have another series of atoms with 'A' altLoc followed by a series
of atoms with 'B' altLoc. This is another set of alternate branches in the
chain ... another 'run'.
Finally we end the chain with another series of ' ' (space) altLoc atoms.
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?
Is this a valid confomation?
' '
' '
'A'
'A'
' '
' '
'B'
'B'
'B'
' '
' '
I should not answer the question because I would only be repeating rumors
that I have heard ... and things that I may well have misconstrued.
> What are some more files we can test this on? (1skt is over 30 models
and 5 Mb -- any others?)
Jmol-datafiles/pdb/1HJE.pdb
It looks like to me that it contains 6 (7?) runs with A & B branches.
Miguel
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