Hi Ed,
you are right about the original question, but what I mean is this: if
the occupancies (and B-factors) differ so much in crystals with
IDENTICAL binding sites, i.e. identical affinities, does this not show
that occupancies (and B-factors) do not reflect affinities alone, but
equall
If I understand the original post correctly, the binding sites in
question are not chemically identical. While it's possible that lattice
may invert the order in which sites are occupied, it is not very likely
given that affinity gap is sufficient to be observable by ITC.
Mutagenesis is a good op
Dear CCP4ers,
a post-doctoral position is available immediately in the laboratory of Dr.
Alessandro Vannini, within the Division of Structural Biology at The Institute
of Cancer Research in Chelsea, London, UK. We are looking for highly motivated
individuals with a strong interest in structural
Hello,
we work with proteins that have typically several chemically identical
binding sites (viral capsid proteins fully assembled or as multimeric
assembly-intermediates). Depending on how long at which concentrations
they are soaked the chemically identical ligand pockets within one
asy
Dear Ed,
when it comes to deciding about the high-resolution cutoff, I agree that the
paired-refinement technique should be used - even more so as it does not
require any of the data quality indicators!
But my posting was meant in a more general sense (i.e. not only talking about
high-resol cu
IMHO, while explaining binding affinity from a structure is fun, it does
not prove anything. Assuming that I understand your situation
correctly, you can (relatively) easily find out from experiment which
pocket has higher affinity. Just do soaks with different ligand
concentrations - the expecta
Dear Kay,
I wonder what is your opinion of the following proposition.
"None of the data quality indicators derived from data alone matter too
much".
Let me explain what I mean by this.
Ultimately, I truly don't care what value of Rmerge, Rpim, or even CC1/2
data processing produces from the set
Hi Jim,
of course the issue of crystallographic data quality indicators deserves a
somewhat more appropriate (or at least more permanent, and peer-reviewed) means
of dissemination than CCP4BB. Nevertheless I'll sum up some of the most
important points I can think of:
A) all data quality indica
Graeme wrote:
"... Rpim is much more instructive. ... as each of these tells something
different."
I have to ask:
"Why is Rpim much more instructive? I'm trying to figure this out still. Can
one please summarize what are best practices with all these numbers and how
each of these tells someth
Dear Niu,
concerning XDS: there is no way, using just XDS.INP, to force the IDXREF step
to use a cell that is not compatible with the reflections that COLSPOT found.
But I can think of two ways to reach your goal (even if I believe that
crystallographically it makes no sense to ignore every seco
You would get a different MR solution in P41212 than in P43212 so you
shouldnt test the SAME pdb in both SGS?
Not sure I am understanding this though.
Eleanor
On 19 November 2013 05:02, #CHEN DAN# wrote:
> Hi Eleanor,
>
> I checked P43212 and P41212 by changing the header of mtz file and running
Dear Tobias,
What exactly do you mean with "I can't get it to work" ? Do you get an
error message or does the program simply compare the 100 SHELXD
substructures against an ever-extending unique set (hence ignoring the
command)?
I just checked myself with the Linux version 0.17.3 (which is the
I've generally found that adding lines to the "standard" table works, and they
are not removed by editors
On 19 Nov 2013, at 09:32, Tim Gruene wrote:
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> Dear Graeme,
>
> On 11/19/2013 09:02 AM, Graeme Winter wrote:
>> [...] For the merged I/
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Dear Graeme,
On 11/19/2013 09:02 AM, Graeme Winter wrote:
> [...] For the merged I/sig(I) Rpim is much more instructive. I'd
> love it if people reported merged and unmerged I/sig(I), Rmerge,
> Rmeas, Rpim, CC1/2, ... as each of these tells something
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Dear Niu,
in XDS the respective keywords in XDS.INP are "REFINE(IDXREF)",
"REFINE(INTEGRATE)" and "REFINE(CORRECT)".
If you do not want the cell to be refined, you have to set all three
keywords (i.e. ensure they are not commented out with a leading
Usually this means that you have relatively high multiplicity, which
give-or-take improves the I/sig(I) by sqrt(m) where m is the multiplicity,
but also increases the Rmerge.
For any given narrow shell of reflections,
Rmerge ~ 0.8 / unmerged(I/sig(I))
merged(I/sig(I)) ~ sqrt(m) * unmerged(I/sig(
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