It seems this happens at the level of the refinement programs. Both seem
to convert to C2, but use the I2 cell parameters. They are somewhat
older versions, so perhaps it is an old bug and not a new one? I've
confirmed that the input mtz I used for both refmac and phenix.refine
was in I2 with the appropriate cell parameters. Here are the versions
and relevant log output:
Refmac 5.8.0124:
Cell from mtz : 25.970 46.960 35.974 90.000 101.152 90.000
Space group from mtz: number - 5; name - C 1 2 1
phenix.refine 1.9.1692:
Working crystal symmetry after inspecting all inputs:
Unit cell: (25.97, 46.96, 35.9742, 90, 101.152, 90)
Space group: C 1 2 1 (No. 5)
Removing 9971 systematic absences:
Average absolute value of:
Absences: 12548.1
Others: 12340.5
Ratio: 1.01683
Other versions of programs used:
Phaser 2.5.7
Pointless 1.9.33
Aimless 0.5.12
C2 cell: 40.08 46.97 25.98 90 118.27 90
--paul
On 11/04/2016 08:05 AM, Phil Evans wrote:
Where does this problem arise? I was under the impression that I2 was
acceptable everywhere (which is why Pointless follows the IUCr guidelines in
preferring I2 over C2 if the beta angle is smaller)
Everything should work in I2: if it doesn’t it’s a bug (similarly with space groups
such as P 2 21 21 with a<b<c)
Phil
On 4 Nov 2016, at 12:00, Paul Paukstelis <shocksofmig...@gmail.com> wrote:
Thanks to all that responded. I sorted this out.
It all appears to stem from the C2->I2 conversion. Forcing everything in
processing to stick with C2 fixes all the issues!
Thanks again,
--paul
On 11/03/2016 12:39 PM, Paul Paukstelis wrote:
CCP4BB,
I posted some time back about a DNA oligonucleotide structure we were working
on. I had difficulty phasing it despite strong signal from bromines, but
finally managed to get reasonable enough maps from a few datasets to build,
only to find that despite the density looking quite good, it simply wouldn't
refine past R/Rfree of around 28/32. With help from ccp4bb it began to become
clear that this might be a candidate for a lattice with translocation defects.
I had my student make a variant in which two 3' nucleotides that weren't
involved in base pairing contacts were removed. This crystallized under the
same conditions in a different space group and was now diffracting to ~1.0 A
(from about 2.2 in the previous space group). Images overall looked good,
though we collected on some crystals that clearly had more than one lattice
that made indexing more difficult. The best looking data still had some tails
on spots, but was easily indexed in C2, which Pointless quite happily changed
to I2 to minimize the beta angle. There are no clear alternating strong/weak
intensities. Phaser finds a strong solution using the previously built dimer,
but notes a 25% over origin peak in native Patterson. Maps look very good,
though after the first round of refinement it is apparent that there is another
dimer in the ASU, but it is clearly overlapping the first. If I'm not mistaken,
all these clues suggest lattice translocation defects. Question 1: any thoughts
on how likely it would be for a molecule to intrinsically pack in such a way
that it results in lattice translocation defects?
I thought it would be worthwhile pressing on given the high resolution it would
be possible to do grouped occupancy refinement of the dimers without taking too
huge a hit in observation/parameters. Refinement with refmac using occupancy
groups leads to a best R/Rfree of 18/24, though geometry could be better in
some spots. Curiously, refmac (or phenix.refine) in the PDB header reports only
50% completeness in the resolution range, though all the data reduction and
analysis (aimless, xtriage) report 99% completeness. Question 2: Why is this?
Phenix logfile says something about removing about half the reflections as
systematic absences. I have been working with everything in I2 after Pointless
switched it over.
Question 3: Any other suggestions on how to proceed with refinement in a case
like this? My gut instinct tells me that it would be better to not do intensity
correction due to the high resolution, but perhaps that's something to pursue?
Thank you in advance.
--paul
