Post-Doc Position: Structure-aided redesigning of an enzyme: molecular biology,
protein expression/purification & crystallography
Immediate opening, in the Sussman lab at the Weizmann Institute of Science,
for a postdoctoral fellow with experience in cloning and in protein expression,
purifica
Jim,
This is coming from someone who just got enlightened a few weeks ago on
resolution cut-offs.
>>I am asked often: What value of CC1/2 should I cut my resolution at? <<
The K&D paper mentioned that the CC(1/2) criterion loses its significance at ~9
according to student test.
I doubt that
Dear CCP4bb,
almost 12h have passed since I posted this question to the board. Since some of
us get daily or weekly digests I will hold off with revealing the results. But
the replies thus far are really interesting and exciting, and this is without
any sarcasm tags. However we have only sample
>
> The deadline for Jan/July 2014 Collaborative
> Crystallography proposals will be *Sep 4, 2013. *
>
>
>
> Through the Collaborative Crystallography Program (CC) at the
> Advanced Light Source (ALS), sc
On 22 August 2013 07:54, James Holton wrote:
> Well, yes, but that's something of an anachronism. Technically, a
> "Miller index" of h,k,l can only be a triplet of prime numbers (Miller, W.
> (1839). A treatise on crystallography. For J. & JJ Deighton.). This is
> because Miller was trying to
I am pleased to hear that Table 1 has finally entered the realm of
politically incorrect terms. Let me fire another insult at it:
> The data statistics are an attempt to describe the quality of the actual
data as a result of an experiment.
Unfortunately, table 1 does not achieve that objective. T
Hi all,
I wonder when the term 'Table 1' entered Newspeak. I heard students use it
rather recently, and to me it sounds derogative, as though they would treat that
table as a black box generated by some program and better not look at it.
The data statistics are an attempt to describe the quality
> what if the reviewer has no clue of these things we call structures ? I think
> for those people table 1 might still provide some justification.
Someone who knows little about structures probably won’t appreciate the
technical details in Table 1 either
J rgen
Sent from my iPad
On Aug
The RCSB Protein Data Bank (www.rcsb.org) is a publicly accessible information portal for
researchers and students interested in structural biology. At its center is the PDB archive-the sole
international repository for the 3-dimensional structure data of biological macromolecules. These
str
Since we keep discussing resolution cutoffs and the benefits of not to include
all data etc.
I thought I would crowd source your opinion on this particular data set.
processed with XDS, here's the XSCALE.LP output:
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RE
Hi,
a random thought: the data resolution, d_min_actual, can be thought of as
such that maximizes the correlation (*) between the synthesis calculated
using your data and an equivalent Fmodel synthesis calculated using
complete set of Miller indices in d_min_actual-inf resolution range, where
d_mi
Dear all,
registration is currently open for the postgraduate certificate
course in Protein Crystallography via the web at Birkbeck that begins on
Monday, October the 7th. It is for the duration of 1 year during which all
aspects of protein crystallography will be covered from the funda
What a statement !
Give reviewers maps, I agree however, what if the reviewer has no clue of these
things we call structures ? I think for those people table 1 might still
provide some justification. I would argue it should go into the supplement at
least.
Jürgen
Sent from my iPad
On Aug 28,
> We don't currently have a really good measure of that point where adding
the extra shell of data adds "significant" information
> so it probably isn't something to agonise over too much. K & D's paired
refinement may be useful though.
That seems to be a correct assessment of the situation and
Aimless does indeed calculate the point at which CC1/2 falls below 0.5 but I
would not necessarily suggest that as the "best" cutoff" point. Personally I
would also look at I/sigI, anisotropy and completeness, but as I said at that
point I don't think it makes a huge difference
Phil
On 28 Aug
Hi all,
If I am not wrong, the Karplus & Diederich paper suggests that data is
generally meaningful upto CC1/2 value of 0.20 but they suggest a paired
refinement technique ( pretty easy to perform) to actually decide on the
resolution at which to cut the data. This will be the most prudent thing
We don't currently have a really good measure of that point where adding the
extra shell of data adds "significant" information (whatever that means.
However, my rough trials (see http://www.ncbi.nlm.nih.gov/pubmed/23793146)
suggested that the exact cutoff point was not very critical, presumably
>Based on the simulations I've done the data should be "cut" at CC1/2 = 0.
>Seriously. Problem is figuring out where it hits zero.
But the real objective is – where do data stop making an improvement to the
model. The categorical statement that all data is good
is simply not true in practic
18 matches
Mail list logo
