sorry, clicked too fast there. I'll read on....
So something like this (if you prefer to predefine things):
set defaultAltLoc 1A 2B 3B 4C
load "filename"
Heaven forbid that on top of that there are multiple models with
multiple altlocs, but that might be handled with slashes. These could
be easily turning into an int[].
> Another twist ... for this problem in particular it seems to me that
> people would want to load them up and look at them in order to evaluate
> whether or not they make sense. So it seems like forcing them to choose
> which one they want to see before they can see it seems like a problem.
Hmm. Yes. If you go with the premise that someone will want to rapidly
switch between alternative locations, then the thing to do might be to
load it all and then select out the locations for display.
Autobonding shouldn't be a problem -- just don't ever connect AltLoc
nX (n atomno, X AltLoc) with AltLoc mY if there exists an mX.
Yes, I suspect this is the more flexible way to go. Then you would
select altloc=A
meaning always "locations with only the default or specifically A".
That wouldn't be so bad.
How are different "runs" specified?
Bob
Miguel wrote:
A protein is a long chain
A segment of the chain may have a string of atoms that can appear at
multiple locations. I have called this a 'run'.
Within the PDB file these 'alternate locations' (altLocs) are identified
by an alpha character. The default is a ' ', the first altLoc is generally
'A', the second is 'B', etc.
There can be more than one 'run'.
The set of all possible models is the combination of all altLoc runs
paired with all other altLoc runs.
Say that I have a chain that looks like this
' '
' '
' ' OR 'A' OR 'B' OR 'C' # 4 possibilities for this run
' '
' ' OR 'A' OR 'B' # 3 possibilities for this run
' '
' '
' ' OR 'A' OR 'B' # 3 possibilities for this run
' '
There are 4 * 3 * 3 = 36 possible conformations for this protein. (perhaps
some combinations would not work because of interference between atoms,
but that is not my issue).
So, it seems to me that we need a syntax that says something like ...
choose 'A' out of the first run, ' ' out of the second run,
and 'B' out of the 3rd run.
We need a syntax that describes what all of the possible combinations are,
and a syntax for the user to describe which combination they want to see.
Miguel
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
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"Imagination is more important than knowledge." - Albert Einstein
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