[phenixbb] alternate conformation clashes
pafonine at lbl.gov
Thu Jun 14 11:50:42 PDT 2012
altloc canbe used as a way to manipulate occupancy refinement and
non-bonded interactions. The rule is:
- see each other via non-bonded:
altloc " " <> altloc " "
altloc "A" <> altloc " "
altloc "A" <> altloc "A"
- do not see each other via non-bonded:
altloc "A" <> altloc "B"
If you have a molecule on a symmetry element then there is a special
(additional) way to turn the symmetry non-bonded interactions off.
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.
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
I'm not aware of any consensus here (which obviously doesn't mean it
All the best,
On 6/14/12 8:53 AM, Timothy Springer wrote:
> 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.
> 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?
> 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.
> I find it to be less confusing if we switch the conformation names in
> loop 2. What is the consensus view?
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