Hi Gerard,
> On 22 Feb 2021, at 19:38, Gerard Bricogne wrote:
>
> Did you perhaps deposit only part of the data you collected for the
> remote wavelength? For example, only one of several orientations that you
> might have collected in order to try and fill the cusp?
data_r2xgfsf in the 2xgf-s
Hi Gerard,
fortunately I still have the data for this structure on my computer - and not
on tape or somesuch.
Below is the summary of the SCALA logfile, from which the statistics were
quoted. Collection was a single sweep of 180 degrees. I'll send you privately
the complete log file and the out
Dear Patrick, Mark and colleagues,
Examining the data associated to PDB entry 2XGF using the PDBpeep
server, i.e. at
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=2xgf
shows a large region (marked up in dark blue) of missing measurements where
the analysis of the trends i
Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB
archive (http://wwpdb.org/pdb50).
The inaugural symposium will be held virtually on May 4-5, 2021.
The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day.
The event will be recorded and made a
We have a 3 year postdoc position available in the group studying structural
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Hi Patrick,
couldn't see any text in you email, just the subject and the picture, but 2XGF
is our T4 long tail fibre tail tip structure from 2010.
(2XGF stands for "2nd eXtraordinary Great Fibre", at least that's what I
*modestly* imagine..).
I think it's probably one or more of:
- noise (was t
Depending upon the amount of radiation exposure, the iron might be reduced (or
more likely, in a mixed oxidation state) by the X-ray beam.
Diana
**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Cent
Sorry, in my previous email I was oblivious to the fact that there was Fe.
Iron is almost certainly oxidized. So, if you started collecting data with
reduced iron, but it got oxidized during data collection, you are probably
using the parametrization for the reduced rather than oxidized one in the
Is the oxidation state of the coordinated atom, or the identity of that
atom correct?
If there was a very slightly bigger atom, it would take care of the
positive residual density and would push out the His side chains a little
bit, which in turn could take care of the negative ones.
Or, the same e
Hi,
as others pointed out electron rich elements tend to amplify imperfections
visible in Fo-Fc maps. Consider:
- refining occupancy of Fe, the site may be partially occupied;
- refining f' and f'' if data are anomalous;
- surrounding histidines may 'see' this Fe as a nonbonded interaction and
thu
Hello, there usually is noise in the difference map near electron-dense
elements. Maybe refining against I(+) and I(-) might help, as someone suggested
a few months ago or perhaps you have already done that. It would be interesting
to know if it helps. Cheers, Jon.C.
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Dear Colleagues,
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"From data collection to structure refinement and beyond" will be held on June
14-25, 2021 at the Advanced Photon Source (APS), Argonne National Laboratory
(ANL), near Chicago, Illinois, USA. All det
Well - that doesnt look too bad - it is hard to see in a screenshot but
presumably the N & C in the ring are correctly placed?
Why is there positive density over the Fe? Are there other similar
features elsewhere in the map which can be assigned to noise?
Eleanor
On Mon, 22 Feb 2021 at 15:27, Pat
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Dear Tom,
I updated the workstation with Ubuntu 16.04->20.04 This update broke 3d
vision and I am thinking about moving back to Ubuntu 16.04. Other programs
work well.
вс, 21 февр. 2021 г. в 10:59, Folmer Fredslund :
> Dear Tom
>
> Be aware that python2 is currently not supported. It is end-
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