Reprocessing CX data with CrysalisPro

Owned by MX Cluster (Unlicensed)
Last updated: Oct 20, 2022
5 min read

 

At the Synchrotron

There is a Windows computer in MX1 which can be used to process data with CrysalisPro. Unfortunately, it is not yet on the MX network in the same way as the other MX computers, so you need to download your data manually. And you need to copy the data from the computer after your beamtime.

1. Download frames

On the MX windows CrysalisPro processing box, log in via these credientials:

User: mxuser

Password: Beam109Line

via filezilla or similar program, download the frames of the experiment. Instructions

They are in .h5 files, each of which contains 200 egier frames (20 degrees usually). 

/data/mx/EPN/frames/$username/d

where $EPN and $username are the experiment number and the user name, respectively. 

You will need each of the .h5 files, including the master file, for each experiment. 

It is a good idea to make a new folder for each collection, if you didn't do this during data collection. 

At Home

1. Download frames

Via filezilla or similar program, download the frames of the experiment. Instructions

Frames in folder: /data/mx/EPN/frames/$username/d

Frames are in .h5 files, each of which contains 200 egier frames (20 degrees usually). 

where $EPN and $username are the experiment number and the user name, respectively. 

You will need each of the .h5 files, including the master file, for each experiment. 

It is a good idea to make a new folder for each collection, if you didn't do this during data collection. 

2. Convert h5 files to cbf (on windows computer at MX1)

  • On the desktop, open the eiger2cbf_GUI.py shortcut

  • Fill in the boxes with information about your frames. eg.

  • Click start. The frames will start converting. When an info box pops up saying “Program completed successfully!”, your frames are ready to open with CrysalisPro.

 

Optional:

If you want to run eiger2cbf manually so you can select which frames to convert, eiger2cbf is in the PATH, so open a terminal and type eiger2cbf. See eiger2cbf GitHub for instructions.

2. Convert h5 files to cbf (at home)

Things you will need:

In the folder for a collection/dataset:

  • Open a terminal. This can be Powershell or Command Prompt (on Windows).

    python eiger2cbf_spawn.py [name of master h5 file] [number of instances to spawn] [filename stem for CBF]

  • Unless eiger2cbf_spawn.py is in the same folder, you will need to include the path to it in the command. 

  • It is a good idea not to end the filename stem for CBF with a number, because the frame number will be added to this. 

  • In general, use 17 instances to spawn. If you add test to the end of the above command, it will tell you the fastest number of instances to spawn. 

  • For example:

    python "C:\Users\boers\Documents\eiger2cbf\eiger2cbf_spawn.py" Thr_run1_master.h5 17 Thr_run1

 

 

Optional:

If you want to run eiger2cbf manually so you can select which frames to convert, open a terminal and type eiger2cbf. See eiger2cbf GitHub for instructions.

CrysalisPro data processing (at Home and Synchrotron)

To download your own version of CrysalisPro you will need to register for the Rigaku X-ray forum: Rigaku Oxford Diffraction forum

3. Importing data

  • Open an offline copy of CAP (use any old dataset to get it open).

  • Open the import icon on the left

  • Use the known image format

  • Choose Dectris. Select your first frame, then click “Save run file”. The program will then popup a box showing the parameters that it has found in the master file, which can be changed here if they are incorrect (they are correct in my example).

  • The program will then generate frame aliases, and finally popup a window so the newly created dataset can be opened in CAP

  • Click “Open selected”, or double click the line.

  • You will then get an alert to set basic settings for the experiment:

  • Click OK, then on the next window, make sure Small Molecule is selected, and click “Edit options”:

  • It is usually sensible to turn on “Smart background during reflection integration” and “Single wavelength data red”

  • Now you should be able to see the first diffraction image. The beamstop shadow can be seen coming from the centre of the diffraction pattern.

  • Open up the command window (CMD on the left-hand side of the window), move the command window to the right so you can still see the beamstop shadow, then click “Options RED”. Also make sure this window isn’t covering the beamstop shadow on the image.

  • Go to the “Beam stop” tab, and tick the “Put beamstop overlay on” box:

  • The beamstop can now be seen. It is currently set to “Top”, which is clearly incorrect. As the beamstop is not at a nice perfect orientation, we need to set it to “User”, then adjust the parameters: Diameter = 0.7, Angle=178 (this may change if the beamstop is moved), Holder diameter=2.2. Adjust the X- and Y-offset if necessary.

  • The data can now be processed as normal.

For more information on using CrysalisPro, see the User Manual, particularly section 4.5, and section 7.