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(New page: == Hints for using SHARP == Data preparation: - 'unmerged and unscaled' is for SCALEPACK files ( no merge original index) - 'merged and unscaled' for data arising from several separate...) |
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Full documentation for SHARP/autoSHARP is at https://www.globalphasing.com/sharp/wiki/. | |||
== Hints for using SHARP == | == Hints for using SHARP == | ||
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Data preparation: | Data preparation: | ||
* 'unmerged and unscaled' is for SCALEPACK files ( no merge original index) | |||
* 'merged and unscaled' for data arising from several separate conversions to MTZ files | |||
* 'merged and scaled' if there is a single MTZ with scaled datasets | |||
MAD: for the different datasets corresponding to different wavelengths, use identifiers 'peak', 'infl', 'hrem' and/or 'lrem' instead of 'w1' 'w2' and so on. This has the advantage that in autoSHARP, for running SHELXC, the wavelengths can be inferred from the identifiers (instead of from f' and f" which sometimes fails). | MAD: for the different datasets corresponding to different wavelengths, use identifiers 'peak', 'infl', 'hrem' and/or 'lrem' instead of 'w1' 'w2' and so on. This has the advantage that in autoSHARP, for running SHELXC, the wavelengths can be inferred from the identifiers (instead of from f' and f" which sometimes fails). | ||
Since CCP4 6.1 there is a autoSHARP GUI in ccp4i - you just need to | |||
% source /where/ever/sharp/setup.csh | |||
- or - | |||
% . /where/ever/sharp/setup.sh | |||
% ccp4i | |||
== Hints for using autoSHARP on the commandline == | |||
For a hexamer in the ASU use | |||
run_autoSHARP.sh \ | |||
-seq my.seq \ | |||
-spgr myspgr \ | |||
-pdb my.pdb \ | |||
-ha "Zn" \ | |||
-nsit 2 \ | |||
-wvl 1.26515 -mtz mysad.mtz | |||
The order of keyword/parameter pairs matters! Use "-nsit 2" if my.seq refers to a monomer with 2 Zn - or "-nsit 12" if it has 6 monomer sequences. Give 6 monomer sequences if you ''know'' it is a hexamer. | |||
Latest revision as of 19:09, 30 April 2017
Full documentation for SHARP/autoSHARP is at https://www.globalphasing.com/sharp/wiki/.
Hints for using SHARP[edit | edit source]
Data preparation:
- 'unmerged and unscaled' is for SCALEPACK files ( no merge original index)
- 'merged and unscaled' for data arising from several separate conversions to MTZ files
- 'merged and scaled' if there is a single MTZ with scaled datasets
MAD: for the different datasets corresponding to different wavelengths, use identifiers 'peak', 'infl', 'hrem' and/or 'lrem' instead of 'w1' 'w2' and so on. This has the advantage that in autoSHARP, for running SHELXC, the wavelengths can be inferred from the identifiers (instead of from f' and f" which sometimes fails).
Since CCP4 6.1 there is a autoSHARP GUI in ccp4i - you just need to
% source /where/ever/sharp/setup.csh - or - % . /where/ever/sharp/setup.sh % ccp4i
Hints for using autoSHARP on the commandline[edit | edit source]
For a hexamer in the ASU use
run_autoSHARP.sh \
-seq my.seq \
-spgr myspgr \
-pdb my.pdb \
-ha "Zn" \
-nsit 2 \
-wvl 1.26515 -mtz mysad.mtz
The order of keyword/parameter pairs matters! Use "-nsit 2" if my.seq refers to a monomer with 2 Zn - or "-nsit 12" if it has 6 monomer sequences. Give 6 monomer sequences if you know it is a hexamer.