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 <[email protected]> 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
