As an update, this approach did not work in Refmac, but as Pavel
suggested it worked fine with phenix.refine.
--paul
On 08/23/2013 11:51 AM, Tim Gruene wrote:
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Dear Paul,
have you actually tried using the 'alternate location indicator' with
two different residues? I would not be surprised if that would work
with refmac.
Best,
Tim
On 08/23/2013 05:39 PM, Paul Paukstelis wrote:
Greetings,
We have been working on a few DNA crystals in which the asymmetric
unit contains a stoichiometric (or nearly so) mixture of two
similar but distinct oligonucleotides. The resolution is medium to
low (2.7-2.8) but for a few of these there are some hints from the
density for two different bases at the same position. I'm curious
what the best way to approach refinement would be in this case.
Alternate conformation doesn't really work since the residues have
different nucleobases. Having two complete chains with 0.5
occupancy is overkill since there are only 2 (or 4) positions in
which the sequence differs. I tried just adding a second chain for
the varying residues at 0.5 occupancy and adding link records to
the original chain, however this doesn't seem to respect geometry
of the phosphodiester for the flanking residues. I would appreciate
suggestions or any examples in the PDB that might set me in the
right direction.
--paul
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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