Clearly, it is a good idea to keep hydrogens:
http://phenix-online.org/presentations/hydrogens.pdf
Not sure why this keeps coming up as a topic given how much it was said
about it in the past, all the MolProbity arguments, etc..
Issue of missing side chains and loops is tricker indeed.
Pavel
Hi everyone,
This is a friendly reminder to draw your attention to a call for the
International PhD program of the Integrative Molecular and Cellular Biology
(IMCBio) graduate school at the University of Strasbourg, France:
http://imcbio-phdprogram.unistra.fr
The IMCBio graduate school builds
On 3/2/2020 10:12 AM, Alexander Aleshin wrote:
> Dear Dale,
> You raised a very important issue that has been overly ignored by the
> crystallographic community. The riding hydrogens are just a tip of an
> iceberg. It is absolutely unclear even to an experienced crystallographer how
> to treat
Dear Thomas,
Thank you for the explanation. I use an old version 1.7.2.3, and I believe that
the problem is fixed in a newer one. What about residues with missing side
chains? How are they treated when a surface is calculated? I began placing the
"riding side chains" into my models to avoid
ON BEHALF OF DIAMOND LIGHT SOURCE– LIFE SCIENCES :
Dear Colleagues,
In light of the rapidly changing situation world-wide resulting from the
COVID-19 virus Diamond would like to ensure that it is doing everything
possible to support researchers in their efforts to discover more about the
Dear Dale,
You raised a very important issue that has been overly ignored by the
crystallographic community. The riding hydrogens are just a tip of an iceberg.
It is absolutely unclear even to an experienced crystallographer how to treat
poorly ordered side chains or even whole residues. As a
--
Postdoctoral positions at Cold Spring Harbor Laboratory
--
The Furukawa Laboratory at Cold Spring Harbor Laboratory (CSHL) located in the
While we're at it, it would also be a great improvement if the PDB would list
nominal resolution in all 3 directions for structures with significantly
anisotropic data. I'm never 100% sure what to do in those cases.
Thanks,
Phoebe
~~~
Phoebe A. Rice
Dept. of
Dear all,
A PhD position is available in our laboratory at the European
Synchrotron in Grenoble, within the InnovaXN Horizon 2020 MSCA COFUND
programme.
We are looking for a highly motivated student to work on enzymes of
melanogenesis as targets for developing efficient compounds to treat
Dear all,
I have two PostDoctoral openings in my group.
Position #1 - a 3 year PostDoc position in time-resolved crystallography on
membrane proteins, based at the University of Groningen, however the nature
of this position will require a lot of travelling for synchrotron and XFEL
measurements.
Dear all,
We are organizing a summer school in macromolecular crystallography at
Aarhus University and MAX IV Laboratory this summer.
*Dates*: Monday June 8 - Saturday June 13, 2020
*Application deadline*: April 15 (but late applications will be accepted
if there are vacancies)
More
Dear Tim,
I am in agreement with Ethan and you that a complete description of
the restraints and constraints applied to the model should be included
in the deposition. This is currently a major failing of the wwPDB. For
hydrogen atoms we, at least, have the "Riding hydrogen atoms were added"
Dear Guenter,
No, unless you intend to start with MR (option -M0) -- in such case
pointless is not run.
I could add such option, although it may take a while before it's done
and before it goes as an update to CCP4 7.1.
Do you want to skip pointless to save time, or you get wrong result?
Best
13 matches
Mail list logo
