Thanks for the suggestions.
The idea that it's related to a trigonal space group and twinning or
pseudo space group is an interesting one, but this is C2221 and the
intensity stats don't show twinning. Twinned P21 -> C2221 doesn't solve
the non-unit occupancy in this case. Since the other monomers are
full-occupancy it can't be 3 overlapping dimers so the phenomenon is
rather unusual in my finite experience. (Also only one set of Se peaks
for this 4th monomer).
I used Herman's suggestion of finding 3 monomers first (with very large
RFZ/TFZ/LLG since the monomers had been refined against the data) since
that's very fast. And then Phaser took a long while to not find the 4th
monomer. Once I figure out how to make modern versions of phaser to
"fail quickly" like the older versions I'll scan a range of homology%
and see if that changes anything.
Phil
On 12/10/20 9:46 AM, Schreuder, Herman /DE wrote:
Dear Phil,
0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my
mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied
monomers... It may also be related to a (trigonal??) space group...
You probably have already tried it, but phaser has the option to give it
already solved molecules and ask it to search for additional molecules. Here I
would indeed lower the expected % homology significantly, to crudely compensate
for the low occupancy. In contrast to the advice of Dale, I would play around
with the % homology to find the value which works best.
My 2 cents,
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Phil Jeffrey
Gesendet: Donnerstag, 10. Dezember 2020 14:49
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Finding partial occupancy monomer by MR ?
Preamble:
I have an interesting crystal form with 3 monomers (~400aa) at full occupancy and
apparently one at much reduced occupancy. It was built recently from Se-SAD and was in
moderately good condition: Rfree=32% for trimer, 2.6 Å. In recent refinement cycles it
became obvious that there was a 4th monomer in a region of weaker/choppy 2Fo-Fc and Fo-Fc
density that corresponded to a "confusing" set of low-occupancy SeMet sites
found by SHELXD and Phaser-EP. The experimental map was bad in that region and was
probably flattened during density modification anyway, in retrospect.
Question:
Phaser failed to find the 4th monomer after trivially finding the other
3 with a recent version of the monomer. I'm wondering if there's a way to indicate
"this one is partial occupancy" to Phaser, or if there's a way to improve the
odds of success beyond just lowering the expected % homology. Or if anyone has had
success with other programs. This is perhaps a rare edge case but I naively expected
Phaser to work.
In the end I used the weak SeMet sites to locate the monomer and the occupancy
appears to be around 0.32 in refinement.
Cheers,
Phil Jeffrey
Princeton
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