Dear Graeme,
some points for further clarification-
The CORRECT corrections you mention all depend on the geometric description of
the experiment.
This geometric description of the experiment is refined by CORRECT, to come up
with accurate values for
a) application of polarization correction
Dear Nukri,
The following is my opinion which I think is worth discussion, and are
based on my understanding of what XDS does in the CORRECT step.
Firstly, I tend to find the global refinement in the CORRECT step useful
for getting a good unit cell recycling the orientation matrix etc. for
Actually Pointless knows that the INTEGRATE file is corrected for an
unpolarised beam and recorrects for a synchrotron unless the wavelength is one
of the home source ones. See docs. You can specify explicitly I think
Phil
Sent from my iPhone
On 17 Nov 2014, at 09:44, Graeme Winter
HI Phil,
Yep: I was not clear perhaps but I did say this:
Pointless will also do this but assumes unless given a correct value that
the beam is quite polarized. Mostly: care needs to be taken, particularly
if using a wavelength which may be confused with a lab source...
For others: if you do
Dear Graeme,
Could you elaborate on There are also some subtleties to making (b) work
properly... some more? I have a feeling, from observing the beamline users,
that many choose to use this option. It would be very helpful for them to know
what are those subtleties and how to best make it
Dear Kay
Just to comment on (e) since you say you don't know why anyone would want
to do this, yet this is exactly what xia2 -3d does :o)
I use AIMLESS to merge data already scaled by XDS CORRECT or XSCALE as a
way to get a report on the merging statistics which includes all of the
AIMLESS
Dear Graeme,
good that you set this straight.
I consider getting the statistics output from AIMLESS is a perfectly valid
reason for going e), and as long as this is well-tested (which I'd bet in case
of xia2) it's ok. There is one issue I can see: 99% (obviously my guess could
be wrong; just
Dear Kay
I cannot comment on the accuracy or otherwise of your 99%, but every time I
talk about xia2 or write down what the options do, I try to make it clear
that XDS / XSCALE is used for integration scaling then AIMLESS to merge
the data. I have had an interest for a while in scaling the data
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Dear Wolfram Tempel,
there might be some confusion about terms.
It is correct that xscale scales several data sets together. However,
in crystallography, 'merging' might be the better term for this process.
Crystallographic 'Scaling' is far more
Hi Tim,
this is incorrect.
XSCALE determines the relative scale and B in a first step (this is what you
describe).
It then, in a second step, re-determines all scale factors (exactly as CORRECT
does for the individual data sets), at the exact same supporting points that
CORRECT used. (This
On Wed, 12 Nov 2014 15:32:04 +, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
...
It then, in a second step, re-determines all scale factors (exactly as CORRECT
does for the individual data sets), at the exact same supporting points that
CORRECT used. (This avoids over-fitting which
Hi Kay,
thank you for the clarification. I had understood that using XSCALE
after CORRECT does no harm, but did not understand that the reason lies
in the consistent choice of support points rather than not repeating
what might already having been done.
Regards,
Tim
On 11/12/2014 04:32 PM, Kay
Hello Kay,
you said the o-word, and you are familiar with the inner workings of XDS.
Has the data-to-parameter ratio in even complex scaling models become so
small that a doubling (worst case) of model parameters would be a serious
concern? Could one detect such overfitting by, say, comparing
Hi Wolfram,
it took me a while until I realized that you mean overfitting when you said
o-word.
You can abuse XDS in a number of ways, and I would call them overfitting the
data although that would be using the word in a somewhat strained way:
reducing WFAC1 below 1, decreasing
Hello all,
in a discussion
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901
on this board, Kay Diederichs questioned the effect of scaling data in
AIMLESS after prior scaling in XDS (CORRECT). I understand that the
available alternatives in this work flow are to specify
Hi,
I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail:
Thank you Boaz.
So if CORRECT can do a fully corrected scaling, are there no corrections
that XSCALE might apply to XDS_ASCII.HKL data that are beyond CORRECT's
capabilities?
Wolfram
On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan bshaa...@bgu.ac.il wrote:
Hi,
I actually choose the option
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale
XSCALE
http://www.mpimf-heidelberg.mpg.de/%7Ekabsch/xds/html_doc/xscale_parameters.html
is the scaling program of the XDS suite. It scales reflection files
(typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT
You can take XDS data into Pointless Aimless (the CCP4 Data Reduction task)
either from the unscaled INTEGRATE.HKL or the scaled XDS_ASCII.HKL file (or
files). In the case of a single XDS_ASCII.HKL you don't need to rescale it in
Aimless, though you can if you want.
Aimless uses a similar but
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