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
>
>
>
