Dear colleagues,
We cordially invite you to attend the IST Austria cryo-EM inauguration
symposium, which will take place on October 18, 2019. Please join us for
some exciting talks and posters. Registration is free and we have a
lineup of great speakers: Jan Pieter Abrahams,
Peter Brzezinski,
Pavel,
Thanks for pointing that out.
Based on one dataset, it seems to me that using this kind of maps
"no-fill" as an additional guide can help tracing some side-chains.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physic
FYI,
When FFT is run in the CCP4i interface, the output file destination is
configured incorrectly. Examining the batch file that is created for the
job, it appears that CCP4i ignores the MAPOUT filename and substitutes the
file name of the temporary file, which is (alas) deleted in the last step.
The website http://g4.x3dna.org for the DSSR annotated G-quadruplexes (G4)
in the PDB has been launched. Here are two examples showcasing G4 features
automatically derived by DSSR: http://g4.x3dna.org/entries/6r9l and
http://g4.x3dna.org/entries/5ua3
The 3DNA-DSSR program detects and annotates G4
For the record, phenix.refine always produces two versions of 2mFo-DFc
maps, with and without filling in missing Fobs. The one that opens in Coot
by default is the "filled" map, but you can always load the other one for
comparisons.
Pavel
On Tue, Aug 6, 2019 at 8:34 AM Ivan Shabalin
wrote:
> De
Dear Clemens,
Thanks!
It sounds like a good test to do on the output .mtz and see if there are
any significant changes in maps after these "filled in" coefficients are
removed.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological
There are certainly some problems with REFMAC after an anisotropy
correction. The FreeR flags and D corrections are organised in spherical
shells, whereas the D aniso volume is elliptical..
As Kay points out the REFMAC map coefficient for a difference map is 0 if
there is no measurement so there
Dear Ivan,
On Mon, Aug 05, 2019 at 05:44:56PM -0400, Ivan Shabalin wrote:
> Dear Kay,
>
> Thanks a lot for your answers!
>
> To my best understanding, REFMAC does not have an option of for restoring
> reflections only in certain resolution shells.
Remember that you can always do some simple (bu
Dale Tronrud recently said ' I always like controls.’ in the discussion
concerning water molecules.
So do I but I prefer an alternative to his suggestion, which is the profile of
how the average carbonyl oxygen would look in an F11 map. This is absolute in
the sense that it is full occupancy an
One practically HAS to do what Dale describes. The sigma levels of a difference
map peak depends on how much it is above the mean noise level of the map. With
high resolution (and given a cooperating molecule) it is very likely that the
model is very good and complete, thus low mean map noise le
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Best regar
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