Wiki source code of 11. Data processing
Version 14.1 by hakanj on 2020-12-18 14:57
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4.1 | 1 | \\ |
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2.1 | 3 | **10.1. Automatic data processing** |
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13.1 | 5 | Unless you un-check the option for the specific acquisition run, autoprocessing will be executed. For standard rotational data autoprocessing is via XDSAPP (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: rgb(0,0,0);text-decoration: none;" %)Zhang et al. (2006). (% style="text-decoration: none;text-align: left;" %)//J. Appl. Cryst.//(% style="color: rgb(0,0,0);text-decoration: none;" %) (% style="text-decoration: none;text-align: left;" %)**39**(% style="color: rgb(0,0,0);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. |
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10.1 | 7 | \\ |
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2.1 | 8 | |
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11.1 | 9 | **10.3. Manual data processing onsite** |
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2.1 | 10 | |
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13.1 | 11 | Open a terminal (see session 3.2) and type ssh haspp11eval01. Please do not use the control computers of the beamline (haspp11user01-04) for data processing. |
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2.1 | 12 | |
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13.1 | 13 | Here you can launch crystallographic programs directly //e.g.//: |
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3.1 | 14 | |
| 15 | * for XDSAPP type in the terminal (% style="color: rgb(0,128,0);" %)xdsapp | ||
| 16 | * for imosflm type in the terminal (% style="color: rgb(0,128,0);" %)imosflm | ||
| 17 | * for CCP4 type in the terminal (% style="color: rgb(0,128,0);" %)ccp4i | ||
| 18 | * for phenix type in the terminal (% style="color: rgb(0,128,0);" %)phenix | ||
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13.1 | 20 | \\ |
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12.1 | 22 | **10.4. Manual data processing after your beamtime or during remote session** |
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3.1 | 23 | |
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13.1 | 24 | Manual data processing after the beamtime or during a remote session is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]]. |
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3.1 | 25 | |
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13.1 | 26 | //Accessing data from outside the DESY network~:// |
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3.1 | 27 | In a terminal window: |
| 28 | ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%) | ||
| 29 | ssh username@desy-ps-cpu | ||
| 30 | Give your password when prompted | ||
| 31 | Navigate to data by: | ||
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13.1 | 32 | cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID |
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| 34 | Data is accessible to users who were registered participants to the experiment in Door prior to the beamtime ID being opened at the beamline. If you cannot access the data, please contact your LC or the beamline manager. | ||
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4.1 | 35 | \\//List of software you can use is at~:// |
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3.1 | 36 | (% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%) |
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4.1 | 37 | \\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).// |
| 38 | \\//To use crystallographic programs~:// | ||
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3.1 | 39 | module avail |
| 40 | module load xray # sets the environment for xds and helper GUIs such as XDSAPP | ||
| 41 | module load ccp4/6.4 | ||
| 42 | module load phenix |