How to merge two or more runs depends on the software you used to
process the images. If you used MOSFLM/CCP4, then you would use the
programs REBATCH (perhaps REINDEX) and SORTMTZ to combine the unmerged
mtz files (the ones that come out of MOSFLM) before feeding them to
SCALA. My program Scaler Elves will do this automatically if you just
put the unmerged mtz file names on the command line:
http://bl831.als.lbl.gov/~jamesh/elves/manual/scaler.html
Once they are scaled, by default Elves will merge different
wavelengths separately, but you can run the merge.com script they
produce with "all" on the command line to just average everything
together into one merged mtz file.
You can also feed the unmerged mtz files to POINTLESS and it can be told
to do pretty much the same thing. POINTLESS will also take
XDS_ASCII.HKL files as input, but I don't think it should surprise
anyone that XSCALE was designed to combine data from as many XDS runs as
you like, as well as do zero-dose extrapolation.
If you are using the HKL Research Inc. suite, then you can put the *.sca
files back into scalepack as individual "frames" (which is what you want
to do to check for non-isomorphism), or you can input all the *.x files
into one scalepack run and obtain a single merged *.sca file that way.
There are plenty of other processing packages out there as well, but I
will make no attempt to make this post a comprehensive list. Suffice it
to say, the exact procedure for combining two runs depend on the
software you are using (and the manuals are remarkably helpful).
An important thing that is not done automatically, however, is to check
if your space group has more than one indexing solution. Basically, if
merohedral twinning is possible, then it is also possible that your two
datasets were indexed differently. If so, they will not merge well!
Until you re-index one of them. A nice table to use is here:
http://www.ccp4.ac.uk/html/reindexing.html
Again, POINTLESS can be used to try and re-index one dataset to match a
"reference", but if non-isomorphism is high, then it can be hard to
tell. In general, it is better to merge/average data together when the
sets are isomorphous and it is not a good idea to merge/average if they
are not! How much non-isomorphism is too much depends on how small of a
difference signal you are trying to measure. For example if you are
trying to measure a 3% dispersive difference, then 15% non-isomorphism
is way too much.
It is an under-appreciated fact that radiation damage is a serious
source of non-isomorphism. Banumathi et al. (2006) found about 1%
increase in non-isomorphism per MGy of dose. If you don't know what a
MGy is, then I recommend you have a look at the open-access article:
http://dx.doi.org/10.1107/S0909049509004361
There are plenty of other sources of error as well, and although there
is no a-priori reason to think that data taken from one instrument on
one day would be any different from data taken from the same crystal on
a completely different instrument on a different day, it is never
surprising when they don't merge very well.
By the way, I wouldn't use "MAD" to describe the mergeing of
non-isomorphous datasets. Strictly speaking, MAD is at least an attempt
to measure both anomalous (f") and dispersive (f') differences, and I
don't think it is appropriate to use the term "MAD" when you know the
dispersive signal is washed out by non-isomorphism. I call such
attempts MSAD (mult-SAD), which I think helps differentiate them from
actual MAD data collections where you at least try not to fry the
crystal between measurements that you need to subtract to get your
phasing signal. Unless, of course, you are doing RIP!
Just my humble opinion,
-James Holton
MAD Scientist
On 1/18/2012 3:08 AM, Tim Gruene wrote:
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Dear Arko,
could you not try MAD with the two different data sets?
Otherwise you can check the strength of the anomalous signal for both
sets separately (I am sure pointless prints the anomalous CC over
resolution shell) and after merging them.
If the signal increases, use the merged data set for SAD, it it does
not, use them separately (but then you call it MAD...).
Tim
On 01/18/2012 12:03 PM, arka chakraborty wrote:
Hi all,
I have two datasets, both CO SAD data, one collected at CO anomalous
wavelength at synchroton and the other at home source. I wish to combine
these two data-sets and use for SAD phasing. Can anyone suggest how this
can be done?
Regards,
ARKO
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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