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CX data processing on MX

All data on the MX beamlines is processed with XDS. For more information on XDS you can read the XDS paper or check out the XDS wiki.

Accessing your data on the beamline

The best way to access and analyse your data on the beamline computers is via the Linux terminal. If you are new to Linux, check out the Beginners Guide to Linux {insert link to Linux beginners guide}

The auto processed data can be found in the following directory:

/data/$EPN/home/$PI/auto/dataset/

where $EPN is the experiment number and $PI is the principle investigators surname.

You should see a directory with the form /data/$EPN/home/$PI/auto/dataset/yourexperiment_1_###########

Be aware that a directory is generated every time you screen as crystal, as well as when you collect a dataset. So when processing data, make sure you are processing a full dataset, and not crystal screening. You can check this by checking the run number for your dataset in the processing page, which should be the final number in the folder name.

{Insert picture of processing page and data folder}

Analysing your data on the beamline

For every dataset you collect, there will be 5 hkl files generated. So the first thing you need to do is assess each of them and decide which is most likely to give you the best refinement.

In your dataset folder you will find:

• The autoprocess.cif_mx1 or autoprocess.cif_mx2 metacif file which has all the collection specific information you will need for youf your final cif. For more information in this, see https://asuserwiki.atlassian.net/wiki/spaces/MX1/pages/409993222/CIF+file+entries?moved=true

• The XDS processed hkl file for your data processed in P1 with a multi-scan absorption correction: XDS_ASCII.HKL_p1 P1

• The XDS processed hkl file for your data processed in P1 without an absorption correction: XDS_ASCII.HKL_p1P1_noscaleNOSCALE

• Three folders of data which has had sadabs absorption correction applied: sadabs_w, sadabs_m, sadabs_s. Each will contain:

  • A hkl file: sad.hkl

  • A prp file with unit cell information of the data: sad.prp

  • A log file with infomration information about the absorption correction: sad.abs

  • A hkl file: sad.hkl

  • An autoprocess.cif metacif: eg. autoprocess_sadabs_w.cif_mx1

• A log file with information to compare data quality for the different absorption corrections: rint_log.txt

  • This will contain the resolution, number of spots (#data), theoretical number of spots (#theory), completeness, redundancy, mean intensity, mean intensity/sigma (Mean I/s), R(int) and Rsigma.

  • This is a good way to assess which absorption correction gave has the best data.

  • In the below example we would choose the XDS_ASCII.HKL_p1 to use to solve the structure, because it has the lowest R(int) and the highest Mean I/s. The noscale dataset can definitely be disregarded because it has a very high R(int).

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If your data is incomplete and needs merging, see Dataset Merging

Once you have decided which hkl to use, follow these steps to process your data with XPREP and then solve it with SHELXT:

1. In a terminal, navigate to your dataset folder.

   • If you already have the dataset folder open in file explorer, you can just right click and select ‘Open terminal here’

   • If you want to use the sadabs file, make sure you go into the relevant folder. It will also be helpful to open the sad.prp file so you can copy the cell parameters into xprep.

2. Run xprep in terminal:

   1. Start by typing xprep and hitting enter, which will run xprep as normal, in the terminal

   2. In xprep, call the hkl you want to use. Note that it is case sensitive, and if you use the XDS_ASCII.HKL_P1 file, you need to enter the whole file name, not just the XDS_ASCII.

   3. Run through xprep as normal, selecting the lattice, cell and space group, checking the data quality, entering the unit cell contents, and naming the output files, eg. filename.ins

3. Solve your data with SHELXT in the terminal: shelxt filename (leave off the .ins)

   1. This will give you solved data .ins files (most likely in more than one space group), named filename_a.res, filename_b.res etc and some information about the datasets (can’t remember what exactly…) so you can choose which one looks best

4. Open the initial solution via the terminal, either with shelxle or Olex2 by:

   1. shelxle filename_a.res

   2. Olex2 filename_a.res