Hi,
There is a postdoc position available in Chris Dealwis lab in Case Western
Reserve University, Cleveland, OH, USA. If anyone is interested, please see
the attached mail.
postdoc.doc
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On 09:50 Tue 14 Sep , Dirk Kostrewa wrote:
> I would spend some time in improving the search model, first. If there
> are more than one possible search molecules in the PDB, I usually do a
> structural alignment (ssm superposition) to get an idea about the
> flexibility of the search molecul
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to
announce the "Structure Integration with Function, Taxonomy and Sequence"
(SIFTS) initiative, a close collaboration between PDBe and UniProt, that aims
to improve the integration of the structural database and other bioinform
Very interesting discussion. I wonder if the "inexperienced user" of PDB really
exists? I don't know anyone off-hand who would really make use of information
from hydrogen positions but not understand the issues. Although I hear they
have been sighted in the Everglades http://en.wikipedia.o
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As a relatively inexperienced scientist, I find this discussion
fascinating.
I wonder if NMR and EM people are also worried about depositing enough
"modeled info" to allow back calculation of data.
Regarding the original discussion of whether to deposit riding
hydrogens used in the refineme
Dirk,
- Imagine a (not very uncommon, unfortunately) situation when someone
obtains the final model and Fcalc, and then, right before the PDB
deposition does a final check in Coot, and moves/removes a few atoms
(a few waters, or instance) here and there. Or may be does a
real-space fit of a
> Oh, goodness, I see: even here, we would need clear rules what the
> calculated structure factors are, which weights are were, which bulk solvent
> correction was applied ... a maze, too!
Fortunately the X-ray & restraint weights/target values are not an
issue here: varying them changes the refi
Dear Ian,
Am 17.09.10 12:30, schrieb Ian Tickle:
Dirk
Personally I wouldn't make use of the deposited Fcalcs, I would insist
on having the refined model, not only for the reasons Pavel gave, but
also because it's never clear which mathematical model was used to
produce the deposited Fcalcs. T
Dirk
Personally I wouldn't make use of the deposited Fcalcs, I would insist
on having the refined model, not only for the reasons Pavel gave, but
also because it's never clear which mathematical model was used to
produce the deposited Fcalcs. There are 2 problem areas (at least 2 I
can think of r
Hi Pavel,
Am 16.09.10 17:56, schrieb Pavel Afonine:
Hi Dirk,
so, wouldn't be the deposition of the final model's Fcalc, Phic (and
their weights) along with the final coordinates be the best solution?
The final Fcalc are our best model and can be used to reproduce the
final statistics (whi
Dear Duangrudee,
Thank you for the useful list. Keep in mind however, that the HET codes are
from before the PDB remediation and some of them are now obsolete or (even
worse) refer to a different compound.
Cheers,
Robbie Joosten
> Date: Fri, 17 Sep 2
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