10. Data processing and back up
10.1. Automatic data processing
Results of the automatic data processing are only available during the beamtime. To see the data presenter, open a Browser (Open Terminal and type: firefox) and type /gpfs/current/processed/index.html.
10.2. Download your data during or after the beamtime
Data are available for download via ftp protocol on the Gamma portal as it is described in here.
10.3. Manual data processing during your beamtime
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