Pavel, I have a problem with the number of reflections for refinement
PHENIX report
a. I have almost complete data for the data set - 48071 reflections. I
keep always anomalous pairs separated.
PHENIX reports (using phenix.model_vs_data.log) 94475 reflections
(reasonable, taking into account
My personal experience is ( I frequently re-refine structures I cite
if all the data for that exist
in PDB) that PDB possesses a significant number of artifacts
unsupported by reality but by the wild imagination only. These
artifacts are originated from the modest, good and excellent
la
Dear Dale,
> 1) There is a need for additional validation of structure factor
> depositions.
>
>My recollection is that the output of SF Check is available to
> the depositor via ADIT on the RCSB site. I have found that report
> to be quite helpful in checking for gross errors in my stru
Dear Dale,
On Thu, Mar 12, 2009 at 11:07:05AM -0700, Dale Tronrud wrote:
>This thread has evolved into two different topics. Just to
> clarify:
>
> 1) There is a need for additional validation of structure factor
> depositions.
>
>My recollection is that the output of SF Check is
Hi Dale,
1) There is a need for additional validation of structure factor
depositions.
PHENIX has tools for this:
1) "phenix.cif_as_mtz" will convert the PDB data file with diffrcation
data into MTZ file. It automatically will figure out if the data are
X-ray: Iobs or Fobs, or Neutr
Dear Frank,
Thank you for your answer, as unimitable as ever. We do of course have
to wash one plate at a time when we each feel the pinch of hunger; but as we
do so we should not forget that the PDB is the Central Planning Office, and
that the order for that industrial-scale dishwasher has t
This thread has evolved into two different topics. Just to
clarify:
1) There is a need for additional validation of structure factor
depositions.
My recollection is that the output of SF Check is available to
the depositor via ADIT on the RCSB site. I have found that report
to be qui
Gerard Bricogne wrote:
Looking forward to the archiving of the REAL data ... i.e. the images.
Using any other form of "data" is like having to eat out of someone else's
dirty plate!
That may be so -- but if I'm hungry now, I just pop it in the sink -- I
don't publish a call for tenders o
Dear Eleanor and Gerard,
PDB testing is performed on MTZ file and can not detect conversion
errors.
Wladek
At 10:03 AM 3/12/2009, Gerard Bricogne wrote:
Dear Eleanor,
That is a useful suggestion, but in the case of
3ftt it would not have
helped: the amplitudes would have looked as healthy
Eleanor,
Please note that so far CIF structure factors files were not sent by
deposition site for verification to authors.
I spoke with Helen and John last Saturday and they promised me to change
that policy. Alternatively, one can check his/hers new deposit on every
Wednesday morning.
Best r
Dear Eleanor,
That is a useful suggestion, but in the case of 3ftt it would not have
helped: the amplitudes would have looked as healthy as can be (they were
calculated!), and it was the associated Sigmas that had absurd values, being
in fact phases in degrees. A sanity check on some (recalc
It would be possible for the deposition sites to run a few simple tests
to at least find cases where intensities are labelled as amplitudes or
vice versa - the truncate plots of moments and cumulative intensities at
least would show something was wrong.
Eleanor
Wladek Minor wrot
Dear All,
Dear All,
I just received information from Michael Gao (PDB) that updated sf file
which is scheduled to be released on March 17, 2009 to replace the
current incorrect sf file.
Wladek
Dr. Wladek Minor
Professor of Molecular Physiology and Biological Physics
Phone: 434-243-6865
Fax: 434-982-1616
Dear Michael,
As we already wrote to Helen and John, structure factors for our deposit
(PDB ID 3FTT and RCSB ID RCSB051033) were mis-processed. Currently,
what was pointed on CCP4BB, instead of experimental amplitudes and sigmas
PDB reports calculated amplitudes and phases. Most probably our de
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