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Dear Jacob,
you don't necessarily want to find the global minimum - the global
minimum of the target function might be an overfitted set of parameters.
At low resolution the (local) minimum you do want to reach may not be
very sharp. This is best
Dear all,
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PostDoc Lead Discovery (m/f)
YOUR TASKS AND
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Dear Gregg,
your post raised my curiosity and I look at the map after a round of
refinement with shelxl.
I thought you might be interested in two observations:
1) shelxl refines the occupancy of the 1Q1 ligand to 60% rather than
78% (I don't think
Dear Tim,
Thank you for your quick review of the map, and your reply. Actually,
I always check every water molecule manually one by one before finalizing
my structures because I know that automated algorithms often get them
wrong, and also often place waters in ligand density. I'm away from
Tim,
Overfitting has nothing to do with whether or not the refinement is at the
global (or local) minimum. You can predict how much a model will be
overfitted before you even start the refinement, because it has everything
to do with choices you made or were forced upon you right at the
Dear Ian,
On Fri, Nov 28, 2014 at 11:26:03AM +, Ian Tickle wrote:
[...] Overfitting has nothing to do with whether or not the refinement is at
the
global (or local) minimum. [...]
I don't think I said that.
Let's assume for a moment that you are right and optimisations should be
Dear Gregg and Tim,
Thank you for an interesting discussion and data.
It may be useful to point out, in particular for other readers of the CCP4bb,
that there are a couple of relevant issues (the role of a few missed
reflections on a quality of images and the choice of the cut-off level when
The MX-group at HZB/BESSY II (Berlin) is operating three beamlines for
macromolecular crystallography (see: http://www.helmholtz-berlin.de/bessy-mx) .
These facilities are currently the most productive MX-stations in Germany with
more 200 new PDB-entries annually. The facilities are used by
On Nov 28, 2014, at 00:22, Gregg Crichlow gregg.crich...@gmail.com wrote:
...
The paper now has been published,
...
PDB ID 4K9G.
... The primary citation in the PDB summary is (2014) INT J ONCOL. 45:
1457-1468
... unless any others are worth mentioning here...
-Bryan
Dear all,
i am solving a structure of 2.5 A resolution by PHASER but every time i got
this following warning.
$TEXT:Warning: $$ Baubles Markup $$
-
Large non-origin Patterson peak indicates that translational
Dear all,
i am solving a structure of 2.5 A resolution by PHASER but every time i got
this following warning.
$TEXT:Warning: $$ Baubles Markup $$
-
Large non-origin Patterson peak indicates that translational
Dear all,
i am solving a structure of 2.5 A resolution by PHASER but every time i got
this following warning.
$TEXT:Warning: $$ Baubles Markup $$
-
Large non-origin Patterson peak indicates that translational
Hi,
Working with Phaser in the presence of tNCS is not necessarily as automatic as
in the absence of tNCS. It can be rather complicated, and not all decisions
are necessarily made correctly. So I would suggest reading some new
documentation on this:
Are you testing all SGs? for your known point group?
Eleanor
On 28 November 2014 at 13:34, rohit kumar rohit...@gmail.com wrote:
Dear all,
i am solving a structure of 2.5 A resolution by PHASER but every time i
got this following warning.
$TEXT:Warning: $$ Baubles Markup $$
yes...right know its monoclinic (p21) space gp.
On Fri, Nov 28, 2014 at 7:24 PM, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote:
Are you testing all SGs? for your known point group?
Eleanor
On 28 November 2014 at 13:34, rohit kumar rohit...@gmail.com wrote:
Dear all,
i am solving a
Dear Rohit,
Are you sure about your space group? I think you should look at this first
Hope it helps.
Etienne
Etienne Rebuffet, PhD
Tel: +334 86 97 73 34
Laboratory of 'integrative Structural Chemical Biology (iSCB)'
Cancer Research Center of Marseille (CRCM)
CNRS UMR 7258; INSERM U 1068;
And what is the NC translation vector (in fractional coordinates)?
If it is x, 1/2, z then your SG could be P2 - the NC translation will
generate absences along the 0k0 diffraction vector.
Eleanor
On 28 November 2014 at 14:01, rohit kumar rohit...@gmail.com wrote:
yes...right know its
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Foundation at the Uniformed Services University of the Health
Sciences across the NIH in Bethesda, Maryland, to work on toxin-antitoxin
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Hi Tim,
you don't necessarily want to find the global minimum (...)
this contradicts the definition of crystallographic structure refinement.
If finding the global minimum is not what you ultimately want then either
the refinement target or model parameterization are poor.
Clearly, given
Dear Pavel,
there is a beautiful paper called 'Where freedom is given, liberties are
taken' by Kleywegt and Jones, but also a wide variety of articles that
(fortunately) fought hard for the introduction of Rfree to the
(macro-)crystallographic community.
In there is mentioned the threading of an
On 28 November 2014 at 19:40, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Where freedom is given, liberties are
taken' by Kleywegt and Jones
Tim
First to summarise the correct procedure:
One performs optimisations with one of more starting models. By 'model' I
mean here the mathematical
Hi Tim,
your examples are valid and valuable, and clearly exemplify existing
problems, limitations as well as common misconceptions.
However, if you follow mathematics and strict definitions thereof, then
crystallographic structure refinement is nothing but an optimization
problem that,
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