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11. Data processing

Version 15.1 by hakanj on 2020-12-18 14:59


11.1. Automatic data processing

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 D62 (2006) 48-57) and Spotfinder (Zhang et al. (2006). J. Appl. Cryst. 39, 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.


11.2. Manual data processing onsite

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.

Here you can launch crystallographic programs directly e.g.:

  • for XDSAPP type in the terminal xdsapp
  • for imosflm type in the terminal imosflm
  • for CCP4 type in the terminal ccp4i
  • for phenix type in the terminal phenix


11.3. Manual data processing after your beamtime or during remote session

Manual data processing after the beamtime or during a remote session is only available for registered DESY Science Accounts.

Accessing data from outside the DESY network:
In a terminal window:
ssh username@desy-ps-ext.desy.de
ssh username@desy-ps-cpu
Give your password when prompted
Navigate to data by:
cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID

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.

List of software you can use is at:
https://confluence.desy.de/display/IS/Photon+Science

You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).

To use crystallographic programs:
module avail
module load xray       # sets the environment for xds and helper GUIs such as XDSAPP
module load ccp4/6.4
module load phenix