Hello CCP4 Community,
The 2022-3 run is underway at the APS and we have some openings for November.
If you need some beamtime, please feel free to reach out and we can discuss
openings that might work with your team.
To find out more about what NE-CAT has to offer please see the following:
h
Hi Andy
Yes, ARG side chain should not be planar. It was mistakenly restrained to be
planar. The same rule applies for peptide planes. Planarity should only be
applied (if ever) for aromatic groups. For ARG side chains the bond is sp2-sp2
and rotation around this bond is not as prohibited as ro
HI Robbie and all,
Here is further recent analysis regarding the geometry of Arg side chains and
recommendations for restraints:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709202/
Best, Andy
[Black Lives Matter]
Dr. P. Andrew Karplus (he, him, his)
Distinguished Professor of Biochemistry a
**
*Dear colleagues,*
*
We have expanded the superposition process at the PDBe-KB aggregated
views of proteins to allow superposition of the predicted model from the
AlphaFold Protein Structure Database (AlphaFold DB). This new feature
loads the model from AlphaFold DB on demand and superpos
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Effective Sample Preparation and Novel Purification Methods for Protein
Production and Crystallization
TOMORROW IS THE LAST DAY TO REGISTER!
Join us November 3rd for Effective Sample Preparation and Novel Purification
Methods for Protein Production and Crystallizat
A postdoctoral position is available in the Laboratory of Protein
Crystallography - CIBIO - University of Trento, Italy. The project aims to
generate new classes of tool compounds for cancer drug discovery. Candidates
should have a PhD in a relevant subject area and experience in protein
expre
Hi Fellows/Windows dev experts,
two minor issues on windows install of ccp4i 8.0.005 :
A. the qtRview logs have no tables or graphs, but they offer (slightly
cryptic but plentiful) messages
'Inconsistent number of data records and plain table contents in XRT schema'
How can I f
Hi Garib,
> Are these related to the side chain of ARG? In the monomer library sigmas are
> capped from below - 1.5degree.
> In the PDB these sigmas might be very small and tiny differences could be
> given
> as outliers.
> Another reason might be that in the monomer library these two angles are
Are these related to the side chain of ARG? In the monomer library sigmas are
capped from below - 1.5degree.
In the PDB these sigmas might be very small and tiny differences could be given
as outliers.
Another reason might be that in the monomer library these two angles are
identical (they are
Hi Fellows/Garib,
I notice unexplained discrepancies between the PDB validation report and the
Refmac log file:
a. If I set in 'Monitoring and Output Options' the angle sigma for the
log output reporting option to the PDB 5 sigma cutoff,
I get zero angle deviations (i.e., no angle devi
Dear all,
We have an open PhD student position at the Institute of Bioorganic
Chemistry Polish Academy of Sciences in Poznań, Poland.
The project aims at drug discovery and will employ among others
crystallographic fragment screening.
More details here in the advertisement:
https://portal.ichb.pl
Dear all,
We have two fully-funded open positions, one for a postdoctoral researcher and
one for a PhD student, in our research group located at the University Medical
Center Göttingen and the Max-Planck-Institute for Multidisciplinary Sciences in
Göttingen, Germany.
Our team studies the struc
If you import cif dictionary then in coot mutate residue should work. At least
it worked n one of our problematic cases. If it does not work then Paul Emsley
may be able to help.
Regards
Garib
> On 20 Oct 2022, at 02:06, Jiang Xu wrote:
>
> Hi Garib,
>I deleted the Met residue and import
Hi Jiang,
It could have a lot of causes. What I would first check is that the chainID of
the NLE is the same as from the surrounding protein, that the new NLE has the
same residue number as the deleted MET. I would also check that the position
within the coordinate file is the same as the previo
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