OK yes it's Phaser: the version you are using is not writing the correct
CCP4 space group number in the MTZ header (i.e. the one listed in
syminfo.lib), which will confuse many downstream programs using the CCP4
symmetry library. Phaser is using the space group number shown in ITC-A,
but that
An MTZ file contains the space group name, space group number, and all the
symmetry operators. Space group numbers such as 4005 are an unofficial
undocumented extension to International Tables rules and shouldn't be used
as reliable information. The name or the operators should take precedence
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
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
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
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
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
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
That must mean there is a bug in the reindexing to I2
Eleanor
On 4 November 2016 at 12:00, Paul Paukstelis
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
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
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,
11 matches
Mail list logo