Katarina Moravcevic wrote:
Dear all,
I am refining a structure of a protein in a complex with phosphorylated
ligand (inositol ring). My problem is that after restrained refinement with
Refmac, the ring is distorted in geometrically impossible ways. Could
anybody advise me on how to deal with
Dirk is right. It isnt so much a GUI bug as a feature!
When you press restart for any job the previous parameters are loaded
into the script.
Usually this saves you work, but if you are changing from TLS with
initial B fixed to 20 to restrained refinement it is undesirable to keep
that
Dear Jonathan
this sounds like a known issue with the version on molrep that was
released with ccp4 version 6.1.1 (so if you are having the problem
with 6.1.3 then it has got back in). For some reason we did not get
to the bottom of the file path gets doubled up, /home/caruthej/bo3/
Dear colleagues,
We are organizing an EMBO Practical Course on the Structural Characterization
of Macromolecular Complexes. The course is primarily intended for Ph.D.
students and postdocs engaged in challenging structural projects involving
macromolecular complexes.
WHEN: 31 May - 5 June,
On 01/03/2010, at 08.02, Dale Tronrud wrote:
Dear X-ray Community,
I'm sorry to have dragged you all along on this journey. There is
something to Ian and Marc's arguments but I have been unable to
understand
their point. That is my failure and I don't wish to subject the rest
of you to
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Let me give my input to the confusion :-)
Things that can be counted are integers, and have no unit. They may,
however, have a _nominal_ unit, which can be stripes, apples,
pieces of fruit. Those units are solely used for clarity. For
example, I can have 13 pieces of fruit, but that may be
Dear Ian,
Perhaps I should have made a more explicit connection to your message
in what I wrote yesterday. I do not think there is any paradox, or apples
vs. oranges problem, in this situation.
The structure factor is a count of electrons as X-ray scatterers, so
that the Fourier
On 01/03/2010, at 13.55, Boaz Shaanan wrote:
As for equilibrium constants, I'm somewhat puzzled by your remark on
their lack of units (I'm a chemist by the way). Is the equilibrium
constant (or dissociation constant) of the reaction A+B-AB
identical to that of the reaction: A+2B -- AB2 ? I
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Dear Gerard
I would certainly agree that in general, provided one takes sufficient
care over dimensions and units, paradoxes can never appear. However,
in this particular case I was pointing out the dimensionality error of
writing equations such as f = 10e, and equivalent ones for the
structure
On Monday 01 March 2010, Ian Tickle wrote:
Dear Gerard
I would certainly agree that in general, provided one takes sufficient
care over dimensions and units, paradoxes can never appear. However,
in this particular case I was pointing out the dimensionality error of
writing equations such
Dear Ian,
The iteration seems to be converging :-)) .
Regarding your last paragraph, however, I do not think that we have to
forbid ourselves to call a spade a spade because of possible confusions that
might be caused by misleading abbreviations. If the unit is an electron's
worth
Hi.
I'm a little reluctant to get into this discussion, but I'm greatly confused by
it all, and I think much of my confusion comes from trying to understand one of
Ian's assumptions.
Why are the scattering factors viewed as dimensionless quantities? In
the International Tables (for example,
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The project is within the immunity group and
Hi Silvia, I don't know about sophisticated, but it's certainly interminable!
Whether you need to modify your slides (actually only your 3rd slide
seems to be relevant to the discussion) obviously depends on which
definition you choose to along with. If you use what I can call the
On 01/03/2010, at 20.44, Dale Tronrud wrote:
Morten Kjeldgaard wrote:
On 01/03/2010, at 19.01, James Holton wrote:
personal discourse. If I review a paper that lists electron density
in 1/A^3, I will tell the authors to fix it. If a reviewer
tells me
to change my electron/A^3 to A^-3,
A postdoctoral position is available for NIH-funded research to study
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Dear CCP4BB Community,
I would like to draw your attention to these positions in the Structural
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I will be happy to give more information if you are interested in any of
these positions.
Applications can be made at the Careers Website:
Simbios is pleased to invite you to its 3D RNA Modeling and Simulation workshop.
The structure and dynamics of molecules is central to understanding biological
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