Robbie,
Yes, the thought that the anomalous R free flags
could have something to do with it occurred to me
as well, so I checked. As far as I can see, the
test reflections are evenly distributed between
the + and - sets; they were not selected from the
+ or - set only. For the vast majority of the test
reflections, both Bijvoet mates were measured and
both were flagged properly. For some, however,
only one Bijvoet mate was measured and flagged. It
probably wouldn't do any harm to consolidate the
test flags, discarding the few with only one
measured Bijvoet mate, but I really don't see why
it should be necessary to do so.
For now, I have converted the reflection file into
the CNS format and sent to the PDB, hoping that
they will be able to deal with that one properly.
Bit surprised though that no one has run into that
problem before.
Thanks for your suggestion.
MM
On Dec 16, 2011, at 3:54 AM, Robbie P. Joosten
wrote:
Hi Mischa,
Your mtz file seems to
contain 'anomalous' free R-flags (that is what I
gather from Pavel's post). This is kind of
weird. Do you really want I+ in the work set and
I- in the test set? That would bias your R-free.
If the two flags match (which I really hope),
then you can leave one column out before you
(re)deposit your data. This will hopefully
solves the problem.
Cheers,
Robbie Joosten
Netherlands Cancer
Institute
On 12/15/2011 05:40 PM,
Machius, Mischa Christian wrote:
Y'all,
While depositing a
structure, the PDB 'complained' about my
structure-factor file, saying they don't
contain R-free flags or are otherwise
incomplete. The comment was prompted by their
Refmac R-factor test failing.
The structure-factor
file I submitted came from phenix.refine
(xxx_data.mtz). I am using version 1.7.3-928.
Indeed, using this file
in CCP4 fails with the message:
"CCP4MTZfile: Mtz column
type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz
column type mismatch: SIGI-obs(+) M-Q"
The file contains
anomalous data. I have no problems with files
that do not contain anomalous data.
Needless to say that
Phenix uses the structure-factor file just
fine when reading it back into, say, its
validation utility.
When I use
iotbx.reflection_file_reader, I cannot detect
any anomalies.
I am at a loss as to how
to resolve this issue. I would like to deposit
the data as prepared by Phenix so that the PDB
tools can use them.
Anybody ran into this
issue before? Any ideas for how to resolve it?
Many thanks in advance!
MM
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