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
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