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10. Data processing

Version 11.1 by hakanj on 2020-11-11 16:28


10.1. Automatic data processing

Unless you un-check the option for the specific acquisition run, some basic auto processing will be done for you. For standard rotational data XDSAPP is run, for strategy calculation we use mosflm and spotfinder from the phenix package to process the heat map for the grid scans. The results are compiled into HTML-files to give you a convenient way of checking them. These files live 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. All HTML-files will be contained in your copy of the data.


10.3. Manual data processing onsite

Open a terminal (see session 3.2) and type ssh haspp11eval01. You need to open one terminal and ssh to haspp11eval01 for every program you want to use.

To use crystallographic programs:

  • 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

10.4. Manual data processing after your beamtime

Manual data processing after the beamtime is only available for registered DESY Science Accounts.

Accessing data
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
(you can only access the data your Door account was related to during the data collections. if you did not participate to the beamtime but are part of the group and would like to access the data, please contact (whom? I'll try to figure this out)

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