Jan wrote:
Bob Hanson wrote:
I'd like to start thinking about Phase II in the alternate location
business. Provided my solution at
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm is
sufficient, we next need to think about secondary structure:
Premise: Alternate conformations retain the same chain connectivity.
I don't know an example, but I'm not sure whether an extra residue
(2nd B below) would be allowed or desired?
_ _ _ A versus _ _ _ B B
Certainly this is allowed for heteroatoms. I've seen this several times
-- different number of atoms in "A" than in "B". I'm pretty sure if this
were a protein chain it would be an insertion, not an alternate location.
anyway, it's moot. No longer an issue to worry about.
Premise: A finite number of conformations are represented in any
given CIF or PDB file -- atoms labeled "A" or "1" are all in one
conformation; atoms labeled "B" or "2" are in another conformation.
Atoms not labeled are in all conformations.
moot
Premise: We want ribbons, rockets, and such to display properly for
any conformation in the collection.
done
Premise: Switching between conformations should smoothly render
changes in secondary structure.
done
Premise: Sometimes a change in conformation will reassign a residue
from, say, helix to turn or turn to beta-pleated sheet.
done
Question: Are these three statements accurate?
yes, and in most cases the backbone would be in the common set '% '
Question: Are there more premises we need to work from?
I don't see any.
Regards, Jan
then maybe we are done!
Bob
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