One thing that people often overlook is that quite a lot of protein
can be lost by denaturation on the surface of the drop. This is more
significant for smaller drops. Two suggestions: (1) increase the
proportion of protein in the - technical term - teeny drop to say two
thirds and (2) cover the
Oops.
My link & terminology were a little wayward...
I knew what I meant, but the incorrect link may have proven misleading.
But the answer essentially remains the same:
1) Integrate everything in MOSFLM
2) Enforce consistent indexing using POINTLESS (unless I am mistaken, there
are alternat
I seem to recall hearing Rsym first when I used the Xuong-Hamlin detector,
since there were a substantial number of redundancies. There were two
Rsyms, one called Rrms for the sqrt over the sum of weighted squared
differences and and Rav for the linear summation of unweighted
differences. This was
Hi everybody!
I will appreciate it if anybody can clarify to me the differences
between Rmerge and Rsym. Many thanks, M
Mohammed A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research Building
4500 San Pablo Road
Jacksonville, FL 32
I had learned that Rsym compared symmetry-related reflections within an
image or film (in the context of a rotation exposure), and Rmerge compared
symmetry-related reflections on different images or films with one
another.
Is that wrong?
Bill
Manfred S. Weiss wrote:
> Dear Mohd and all others,
Al's Oil on the plates:
What a nightmare!!!
The oil creeps up the plate and over the sides. It dissolves adhesives.
It makes me say bad words in multiple languages.
Bigger drops + no oil = fewer bad words.
Lisa
--
Lisa A. Nagy, Ph.D.
University of Alabama-Birmingham
[EMAIL PROTECTED]
-O
Dear Mohd and all others,
Well, I guess it is time again to define and talk about R-factors.
The term R_sym goes back to the times, when X-ray data were
recorded by precession photography on film. Except for the central
cone, each reflection was observed only once and R_sym described
the agreemen
On Friday 18 January 2008 09:30:06 am Ethan A Merritt wrote:
>
> Rmerge is an average over replicate measurements of the intensity for
> identical [hkl]. Rsym is an average over the measurements for all symmetry
> equivalent reflections.
>
> In the presence of anomalous scattering, Rsym will be hig
Kay,
I beg to differ, but only in a pedantic way. Historically, Rsym
would refer to the agreement in symmetry-related reflections within a
single data set and Rmerge would be the agreement between 2 or more
data sets that were merged. This was the way we did it back in the
"old day" of
Hello Sun,
Roman Hillig and I refined a mixture of ADP+PO4 and ATP in
the active site of ARL2 - it is enough to exclude all contacts of the
superposing ligands and let the occupancies refine. The protocol we followed is
described in:
Hanzal-Bayer M, Renault L, Roversi P, Witti
Truncate reports I/sigI for reflections in the 30deg cones around the
reciprocal cell axes. Dead handy...
[EMAIL PROTECTED] wrote:
High R "merges" with no reasonable excuse can certainly be a useful
red flag during data processing (along with the % of observations
rejected, which I've never
High R "merges" with no reasonable excuse can certainly be a useful
red flag during data processing (along with the % of observations
rejected, which I've never had a reviewer request).
Which brings up the point that one reasonable excuse is anisotropy -
high Rs for merging random observations
You know there is that other funny column with chi^2's. I like to quote
both. Half of the reviewers will know which column to look at, but you
will satisfy the other half.
Bernie
On Fri, January 18, 2008 1:39 pm, Edwin Pozharski wrote:
> There are two opposing views on this.
>
> First: Rmerge do
Chris Putnam wrote:
I won't belabor this point (or defend this view) any further,
though I will repeat my surprise at the lack of a clear
consensus for what Rsym and Rmerge actually mean,
as opposed to things like I/sigma, for example.
I/sigma is also open to interpretation. Is it / or
(av
Hello everyone,
I have a structure of intermediate state in which about half amount of ATP
decomposed to AMP and pyrophosphate. The ATP and AMP + pyrophosphate have
little difference in conformation, sharing the same electron density.
I just gave them different residue ID and did the
There are two opposing views on this.
First: Rmerge doesn't matter. Don't even look into that column in
scalepack output, you will be upset over nothing. If you collect twice
as much data (360 sweep instead of 180) from the same crystal, your
Rmerge will go up due to higher redundancy, but
Salameh, Mohd A., Ph.D. schrieb:
Hi everybody!
I will appreciate it if anybody can clarify to me the differences
between Rmerge and Rsym. Many thanks, M
there is no difference - unfortunately there are two words for the same
thing. "Rmerge" currently appears to be more in fashion.
just m
Ed,
You don't need to adjust them in XDS.
In scalepack, I don't adjust the individual chi^2's (the additive terms,
by shell), but I do adjust the multiplier to get the chi^2's in the
highest resolution shell, usually with (or /) ~ 1, to be
near and greater than 1.0. Then the overall chi^2's are
On Friday 18 January 2008 11:18:45 am Mischa Machius wrote:
> OK, that brings us back to a more substantial question: is any of
> these R values actually suitable to judge the quality of a given
> dataset? Instead of introducing novel R factors, one could also simply
> ignore them altogether,
Hi Mohammed,
you've put the finger on a weak point in reporting crystallographic
statistics ;-). The use of Rmerge and Rsym differs wi(l)dely amongst
crystallographers. In my opinion, Rsym should be reported for the
single crystal internal symmetry R-factor between symmetry-equivalent
ref
Thank you all, it was very, very helpful discussion. However, I
collected crystal data and the Rmerge overall was very high around 0.17
at 2.6A resolution and I'm wondering what is the acceptable value
(range) of R-merge that worth the time to continue processing! Very
anxious to hear your thoughts
On Friday 18 January 2008 07:50, Santarsiero, Bernard D. wrote:
> I do recall Rmerge being more popular with the small molecule
> crystallographers. However, I also recall a difference between averaging
> over pairs of reflections that were or were not Bijvoet pairs, for even
> small differences i
My understanding is(was) that Rsym refers to the merging of
symmetry-related reflections during scaling whereas Rmerge refers,
broadly, to any data merging process, but originally means merging of
reflection with the same (hkl). Rcryst then should refer to the merging
of data from different cry
Hi all!
Does anybody have experience with crystallization of proteins by slow
drifting of the pH? Let's say, for example, going from pH 7 to pH 5
over 1 week or 1 month. This is supposed to happen by diffusion of
volatile molecules like ammonia or acetic acid but I am having a hard
time f
OK, that brings us back to a more substantial question: is any of
these R values actually suitable to judge the quality of a given
dataset? Instead of introducing novel R factors, one could also simply
ignore them altogether, make sure that the error models have been
properly chosen and loo
On Fri, 18 Jan 2008, Edwin Pozharski wrote:
So Rmerge does tell you something, but only in context with all the
other information.
this is what Whewell termed the consilience of inductions in the 19th
century (which others have expanded since).
-bryan
Bernie,
but my chi-squares are always near 1.0, so why would I report it? How
close they should be to 1 is open to discussion, of course. The point
is, it is assumed (at least in scalepack) that you adjust your error
model until chi-square~1. I have never seen a statistics table in a
pape
In the best case, you would know something about the enzyme bound
equilibrium constant between the two ligand mixtures (see, for example, TM
Larsen et al Biochemistry 35, 4349). That would give you a good sense of
how to model the occupancies of the active site ligands.
Unfortunately, in many ca
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