an mtz file wont have *** - it is a binary file.
mtxdump produces a formatted ascii image of the file,so that could
result in **. That happens when a number you are trying to write is too
large for the allocated format..
Indeed mtz2sca and mtz2various produce an identical sca file give or take a
scale factor…
Eleanor
On 30 May 2015 at 17:29, Phil <p...@mrc-lmb.cam.ac.uk> wrote:
> I thought Aimless automatically scaled things to avoid this
>
> Sent from my iPad
>
> > On 30 May 2015, at 16:47, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote:
> >
> > Dear Eleanor, dear Tom,
> >
> > I wrote mtz2sca specifically for the transit from mosflm to shelx. It
> > automatically scales the data to avoid overflows. I don't remember what
> > it will do when the asterisks are part of the input mtz-file, but you
> > should just give it a try. If it does not work, please let me know so
> > that I can think of a solution.
> >
> > mtz2sca is part of ccp4 now. mtz2various can scale, but needs to be told.
> >
> > Best wishes,
> > Tim
> >
> >> On 05/30/2015 02:13 PM, Eleanor Dodson wrote:
> >> As Harry says, this is a format problem. the sea file only allows
> >> intensities <= 999999.99 .
> >> I thought mtz2various was meant to scale intensities automatically to
> avoid
> >> this, but obviously that hasn't worked.
> >>
> >> You can check from viewing the mtz what the largest intensity is, then
> give
> >> a SCALE instruction to mtz2various to make sure you largest I is below
> the
> >> above limit.
> >>
> >> Is that OK?
> >> Eleanor
> >> Eleanor
> >>
> >>> On 30 May 2015 at 11:44, Harry Powell <ha...@mrc-lmb.cam.ac.uk> wrote:
> >>>
> >>> Hi
> >>>
> >>> You clearly have a very strong (0 0 6) reflection (I ~ |F^2|
> >=1,000,000)
> >>> - it’s overflowing the fixed-width format field in the output of both
> >>> Aimless and mtz2various.
> >>>
> >>> The first thing I would do is to look at the image(s) that the
> reflection
> >>> occurs on - is it actually a reflection from your protein crystal or
> is it
> >>> from something like a satellite ice crystal? In this latter case you
> can
> >>> safely just delete that reflection from the .sca file (but you should
> >>> really re-integrate the dataset making sure the “exclude ice-rings”
> option
> >>> in iMosflm is turned on {snowflake symbol next to the MTZ filename
> entry
> >>> box}, to make sure all spots due to ice are ignored and don’t
> contaminate
> >>> your signal).
> >>>
> >>> I don’t run “mtzdump” very often, but to get the value that Aimless has
> >>> actually calculated for the reflection you could try -
> >>>
> >>> mtzdump hklin <AIMLESS.MTZ> hklout <JUNK.MTZ> <<eof | grep ‘ 0 0
> 6’
> >>> nref 9999999
> >>> eof
> >>>
> >>> where you replace <AIMLESS.MTZ> with the output file from Aimless
> (called
> >>> “aimless_???.mtz in the iMosflm QuickScale option).
> >>>
> >>> I don’t know how the Scalepack format deals with reflections that
> strong -
> >>> that’s one for Phil Evans to address, maybe with help from ZO or
> Wladek.
> >>>
> >>> The immediate way round the problem might be to replace the ******** in
> >>> the .sca file with 999999.9 (use your favourite editor, e.g. vi, emacs,
> >>> pico…) which _might_ be a good enough estimate for you to carry on to
> phase
> >>> (999999.9 would allow a better estimate than just deleting the
> reflection,
> >>> but George Sheldrick would be able to give the best advice on this).
> >>>
> >>> HTH
> >>>
> >>> Harry
> >>> --
> >>> Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick
> >>> Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH
> >>> Chairman of International Union of Crystallography Commission
> >>> on Crystallographic Computing
> >>> Chairman of European Crystallographic Association SIG9
> >>> (Crystallographic Computing)
> >>>
> >>> On 30 May 2015, at 09:45, Tom Wong <wangnan4...@yahoo.co.jp> wrote:
> >>>
> >>> Dear everyone:
> >>>
> >>> Recently I met a mtz format problem: after I processed a data by
> iMosflm
> >>> and scaled by AIMLESS.
> >>> The mtz file could not be processed for further phasing by shelx, it
> said:
> >>>
> >>> ** Input file /home/tom/ccp4test_6_1_sca.tmp.sca corrupted at line
> 7
> >>> **
> >>> 0 0 6******** 38460.7
> >>>
> >>>
> >>>
> >>> Later I use mtz2various program to convert that mtz to sca, i got this:
> >>>
> >>>
> >>> 54.660 75.314 75.314 90.000 90.000 90.000 p 21 21 21
> >>> 0 0 3 72.2 69.2
> >>> 0 0 4 25749.5 1366.3
> >>> 0 0 5 44.4 63.6
> >>> 0 0 6******** 38460.7
> >>> 0 0 7 46.1 62.7
> >>> 0 0 8 1413.8 288.1
> >>> 0 0 9 -2.9 57.4
> >>> 0 0 10424115.3 11976.6
> >>>
> >>>
> >>> I think it is a format conflict problem between iMosflm and shelx.
> >>> Is there anyone who can help me get through this?
> >>> How to do the phasing by using the mtz generated by iMosflm?
> >>>
> >>>
> >>> Thank you very much!
> >>>
> >>>
> >>> Tom
> >
> > --
> > --
> > Dr Tim Gruene
> > Institut fuer anorganische Chemie
> > Tammannstr. 4
> > D-37077 Goettingen
> > phone: +49 (0)551 39 22149
> >
> > GPG Key ID = A46BEE1A
> >
> >
>
