4th model is the fourth model. Eh?
Miguel wrote:
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;
Yes, perhaps something like this would work.
they would come in (in a sense) like vibrations, and
Yes, I see that they have some similiarity with vibrations.
In some ways also seems similar to 'growing a crystal'.
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 is not clear to me what you mean by 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, ....
I am somewhat confused. I don't think that a 'model number' or
'pseudo-model number' is sufficient to describe what needs to be done.
Here is the problem ... as I understand it ...
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.
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.
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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