[ccp4bb]: truncate/ice problems

["David E. Timm" <dtimm@iupui.edu>]

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Here's the summary of suggestions to my problems with ice rings and
TRUNCATE.  Setting RANGE from default (60) to 55 took care of the problem.
Thanks to all of those who responded.

Dave Timm
Indiana Univ. School of Medicine
Dept of Biochemistry
Medical Sciences Building
635 Barnhill Drive
Indianapolis, IN 46202


Use truncate with broader resolution bins. Your bins are now probably so
thin that there are a few with no or perhaps only a few reflections.
Also collect another 360 deg. of data. it will give you a very high
redundancy
and probably the 4.2-3.3 and 2.3-2.2 A bins will be a lot more complete as
well.

Remy Loris


process data with mosflm without rejecting reflections in ice rings.
they will have a stronger background so you can always reject them
later on with sigma criteria. I did that several times and had a much better
map than with my "holy" data set.

good luck

Valerie (Biou)

Hi Dave,
there is a keyword "ranges..." in truncate. If you don't set it - it
will be automatically set to 60 bins. Maybe some of the bins are empty
due to the ice rings.
Maybe it is worth to lower this number.

Greetings
Jan (Abendroth)

Probably can be helped by better data processing.  If you are using Denzo,
adjustment of the parameter "reject slope" to a value like 90 instead of the
default value of 50, will result in less data being rejected due to the
bizarre shape of the background in the vicinity of the ice rings.

Charles A. Hasemann

Hi David,

Just input to truncate the number of bins explicitly.

REduce it by 0.5 the number that it does by default and you will have
enough reflections/bin.

Cheers!

Rams.

Process with Denzo/Scalepack and use to_cns to convert hkl, I, sigI to hkl,
F, sigF.
If necessary, you can than convert the hklf file to mtz using ccp4
utilities.

Alexey Bochkarev

Hi Dave,

Have you tried using truncate only for the good resolution ranges and
then remerging the files in CAD afterwards.  It seems that this would
of course be the long way around, but worth a shot if no better method
arises.

Good Luck,

Christopher L. Colbert

David:

    Maybe problem is in your data integration. If you have Denzo/Scalepack,
try to use keyword "reject fraction". To choose the better fraction to use,
you need to see the images while running integration.
    Probably other packages have similar option(s).
    Hope it helps you.

Ricardo (Aparicio)

You can try to reduce the number of shells in truncate (keyword
RANGES). This is normally not recommended but may help in
such a case.

Good luck!

Karsten Niefind