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Hi Tim,<br>
<br>
altloc canbe used as a way to manipulate occupancy refinement and
non-bonded interactions. The rule is:<br>
<br>
- see each other via non-bonded:<br>
<br>
altloc " " <> altloc " " <br>
altloc "A" <> altloc " "<br>
altloc "A" <> altloc "A" <br>
<br>
- do not see each other via non-bonded:<br>
<br>
altloc "A" <> altloc "B"<br>
<br>
If you have a molecule on a symmetry element then there is a special
(additional) way to turn the symmetry non-bonded interactions off.<br>
<br>
So, as long as you can manage to assign altlocs such that 1) you
achieve desired occupancy refinement behavior and 2) desired
non-bonded interactions, you are fine.<br>
<br>
Conveying this to PDB is a different story, I think. There is a
number of meaningful scenarios where there is no obvious way of
documenting it using altlocs.<br>
<br>
I'm not aware of any consensus here (which obviously doesn't mean it
doesn't exists!).<br>
<br>
All the best,<br>
Pavel<br>
<br>
On 6/14/12 8:53 AM, Timothy Springer wrote:
<blockquote
cite="mid:7CD12AB6-6BC4-43AA-AFF0-F8FDC8DF69B3@idi.harvard.edu"
type="cite">We have a 1.4 Å structure with two pseudo-symmetry
related A and B chains that form a super b-sheet. An 8-residue
loop has two quite different alternate, backbone conformations.
When we refine the occupancy of these loops, they come out to 0.51
and 0.49, consistent with them being mutually incompatible (i.e.,
forced to be 0.50 and 0.50 in the ideal situation). Indeed,
clashes would exist between the A chain A alternate and the B
chain A alternate, but when these are A and B alternates, there is
no clash. Since these are in separate chains, Phenix has no
problem with an A and A clash. There is a second loop,
non-contiguous in sequence, that also has clashes with one of
these. We refine each of the two clashing loops as the A conformat
ion. Since these are separate loops, Phenix does not seem to care
and seems to treat the A conformation of one loop as if it is
compatible with the B conformation of the other loop.
<div><br>
</div>
<div>This is great that Phenix is so forgiving, but my concern is
that shouldn't by convention we reassign the conformations so
that the A conformations are all compatible within the same
monomer? Is there some formal convention on this, and will PDB
ask us to reassign these?</div>
<div><br>
</div>
<div>In a closely related 1.7 Å lattice, we have a single molecule
per asymmetric unit, and now the relationship is between two
symmetry-related molecules. The two conformations of loops are
similar as in the 1.4 Å structure. Here, we have to keep the
same alternate conformation name, and thus have a clash between
A and A loops 1 but not A and B loops 1. Again there is a clash
between A conformation of loop 1 and A conformation of loop 2,
and we could make this go away by switching A and B in loop 2. </div>
<div><br>
</div>
<div>I find it to be less confusing if we switch the conformation
names in loop 2. What is the consensus view?</div>
<div><br>
<div>
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<div>Tim<br>
</div>
</span></span></div>
</div>
</blockquote>
<br>
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