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Hi,
It doesn't necessarily matter for this discussion, but as far as I know,
denzo writes out an x file with unsummed partials, and scalepack will do
the summing. This allows scalepack to refine the mosaicity and adjust
the partiality of reflections.
Johan
Raji Edayathumangalam wrote:
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Here's some notes for you wrt HKL2000 to the extent of my
understanding.
'Partially recorded' reflections for an identical h,k,l, which
can be spread over multiple images, are already 'combined' when
you index and process the dataset in the Denzo component of HKL2000.
During the subsequent scaling/reduction/merging step, two things
happen: 1) multiple observations of a unique hkl are
merged/averaged/combined AND 2) a reflection and its symmetry
equivalents are merged as well.
Since it appears that you have no prior knowledge of the space
group for the data, unless you are confident of the suggested
lattice type, simply use HKL2000 to index, process and scale data
all the way through in P1. Even in P1, the Scalepack default is
to combine multiple measurements of a unique hkl (step 1 above)
but will still be "unmerged" wrt space group symmetry.
But when you specify the 'NO MERGE' option in Scalepack, multiple
measurements of a unique hkl will also not be merged.
In your case, I don't think you need to use the 'NO MERGE' option
in Scalepack.....Unless POINTLESS does not like redundant
observations to be combined. I have never used POINTLESS but I
doubt this is the case.
HTH.
Raji
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Hi All:
I am trying POINTLESS for detecting real space group using data
processed
by HKL2000. Apparently, POINTLESS cries for unmerged data. I
understand
using Mosflm might be the best in this case, but I am not
familiar with
the program.
So I did the following to rescue but not sure if it is the right
thing.
1) Integrate (denzo) as P1 space group in HKL2000. 2) Scalepack
in P1
with keyword "no merge". 3) Using COMBAT in CCP4 to covert to
mtz and
specify the input .sca file as "Scalepack file nomerged (no
partials)".
What I am more curious about, is what exactly does "unmerged"
mean? Does
it mean not reduced to asymmetric unit? Or something happened much
earlier in data processing, like the "no partials" comment in
COMBAT seems
to suggest? If it is the latter case, why is it so important
for symmetry
analysis in POINTLESS?
Regards,
Weikai
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Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224, 1230 York Avenue
New York, NY 10021
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