Ian,
I think I found the issue just by looking through mtzdmp output, but
there was a clue from the response I got yesterday:
Hi Paul,
I have come across this problem before, suddenly what was complete
data is only 50% complete. I seem to recall its because I2 is also
called space group 5 (same as C2), which confuses some programs.
I tracked spacegroup number in the mtz headers. Pointless, aimless,
ctruncate use 4005 for I2. After Phaser (v 2.5.7), the spacegroup number
is just 5. That seemed to be the thing that is bothering refmac and
phenix.refine. For whatever reason I was using the phaser output for the
initial refinement.
--paul
On 11/04/2016 10:58 AM, Ian Tickle wrote:
Paul, mtzdump may not give the full header. The best way to get this
is to use a text editor on the MTZ file (yes I know it looks like
garbage!), scroll to the end where you will find the header starting
at 'VERS MTZ:V1.1'. Then copy/paste everything from there to the end
(don't worry about formatting it).
Hopefully this will give a clue.
Cheers
-- Ian
On 4 November 2016 at 14:49, Ian Tickle <ianj...@gmail.com
<mailto:ianj...@gmail.com>> wrote:
Hi Paul
I just tried Refmac 5.8.0135 (which must be very similar to the
version you are using) with an I2 dataset and I don't see this
"conversion to C2". I doubt very much that the refinement
programs need to convert to C2: I'm pretty sure they can do the
refinement perfectly well in I2.
I think it's much more likely that your MTZ header has somehow got
corrupted with inconsistent space group info so you need to track
back in the history list in the MTZ header and see which program
was responsible for the corruption. Can you post the MTZ header
so we can see the history list and the cell/space group info?
Cheers
-- Ian
On 4 November 2016 at 14:39, Paul Paukstelis
<shocksofmig...@gmail.com <mailto:shocksofmig...@gmail.com>> wrote:
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
