Refmac and phenix.refine versions I used both seem to be problematic.
Both are I2 in and C2 out.
--p
On 11/04/2016 08:25 AM, Ian Tickle wrote:
Hi Paul
This sounds like there might be a recently-introduced bug which should
be reported to the author. I have several structures in I2 & I
haven't noticed anything like this. Can you tell which program is
introducing this error, e.g. by looking at the mtzdump outputs?
Cheers
-- Ian
On 4 November 2016 at 12:00, Paul Paukstelis <shocksofmig...@gmail.com
<mailto: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
