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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
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edited by tabermah
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1 -05. Data processing
1 +07. Data processing
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1 -{{toc/}}
1 += 11.1. Automatic data processing =
2 2  
3 -= 5.1. Automatic data processing =
3 +Unless you un-check the option for the specific acquisition run, autoprocessing will be executed. For standard rotational data autoprocessing is via XDSAPP ([[https:~~/~~/www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/hzb-mx-software/xdsapp3/index_en.html>>url:https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/hzb-mx-software/xdsapp3/index_en.html||shape="rect"]], current version 3.1.9) (Sparta et al. (2016) //J. Apple. Cryst.// **49**, 1085-1092) for strategy calculation we use Mosflm (Leslie //Acta D//**62** (2006) 48-57) and Spotfinder ((% style="color:#000000; text-decoration:none" %)Zhang et al. (2006) (% style="text-align:left; text-decoration:none" %)//J. Appl. Cryst.//(% style="color:#000000; text-decoration:none" %) (% style="text-align:left; text-decoration:none" %)**39**(% style="color:#000000; text-decoration:none" %), 112–119)(%%) for producing the heatmap for the grid scans. The results are compiled into HTML-files to give you a convenient way of checking them. The output files are in the processed folders of the corresponding datasets.  A self refreshing index of all results is created in the beamtimes processed folder. During the beamtime you can open it from file::~/~//gpfs/current/processed/index.html in a browser. The HTML-file is also contained in your data backup.
4 4  
5 -Unless you un-check the option for the specific acquisition run, autoprocessing will be executed. For standard rotational data autoprocessing is via XDSAPP ([[https:~~/~~/www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/hzb-mx-software/xdsapp3/index_en.html>>url:https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/hzb-mx-software/xdsapp3/index_en.html||shape="rect"]], current version 3.1.9) (Sparta et al. (2016) //J. Apple. Cryst.// **49**, 1085-1092) for strategy calculation we use Mosflm (Leslie //Acta D//**62** (2006) 48-57) and Spotfinder ((% style="color:#000000; text-decoration:none" %)Zhang et al. (2006) (% style="text-align:left; text-decoration:none" %)//J. Appl. Cryst.//(% style="color:#000000; text-decoration:none" %) (% style="text-align:left; text-decoration:none" %)**39**(% style="color:#000000; text-decoration:none" %), 112–119)(%%) for producing the heatmap for the grid scans. The results are compiled into HTML-files to give you a convenient way of checking them. The output files are in the processed folders of the corresponding datasets.  A self refreshing index of all results is created in the beamtimes processed folder. During the beamtime you can open it from [[file:~~/~~//gpfs/current/processed/index.html>>file:///gpfs/current/processed/index.html]] in a browser. The HTML-file is also contained in your data backup.
5 += 11.2. Manual data processing =
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7 -= 5.2. Manual data processing =
8 -
9 9  Please do not use the control computers of the beamline (haspp11user01-04) nor the haspp11eval01 for data processing (latter is now fully dedicated to autoprocessing).
10 10  
11 11  Use Maxwell-cluster for data processing as described in the next chapter. Access to Maxwell requires a Scientific Account.
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114 114  Software packages might be available out-of-the box as system installs or as part from the OS default repository, others are available via module functionality. A description on how to enable/use a particular software package is given on [[confluence>>https://confluence.desy.de/display/IS/Software||shape="rect" style="text-decoration: none;"]].
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116 116  (% style="text-align: justify;" %)
117 -Crystallographic software packages are listed in the [[Photon Science and Structural Biology tabs>>https://docs.desy.de/maxwell/applications/||shape="rect"]].
115 +Crystallographic software packages are in the [[Photon Science section>>https://confluence.desy.de/display/MXW/Photon+Science||shape="rect"]].
118 118  
119 119  (% style="text-align: justify;" %)
120 120  You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).