I thought Aimless automatically scaled things to avoid this
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> 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
>
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>
>
