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CX data processing on MX

All data on the MX beamlines is processed with XDS. See Data processingProcessing for more information about XDS on MX. 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 in to Linux

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 principal 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.

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Data Processing webpage

Analysing your data on the beamline

Automated data analysis with CX-ASAP Brute - NEW!

CX data is now automatically run through the Brute pipeline of CX-ASAP which processes the data through XPREP with all recommended options, then through SHELXT. The results of this processing is in a folder labelled “CX-ASAP_Brute” in your dataset folder and contains the results of SHELXT running on the XDS processed hkl and the sadabs absorption corrected files. Therefore, there will be at least four .res files in the folder, cxasap_a.res, cxasap_sadabs_s.res, cxasap_sadabs_m.res, and cxasap_sadabs_w.res.

1. Check the rint_log.txt to compare data quality for the different absorption corrections. 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. 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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2. Open Olex2 or shelxle in a terminal - simply type ‘olex2’ or ‘shelxle’.

3. Open the .res file in olex2 or shelxle by dragging and dropping from your folder.

4. Admire your beautiful structure!

5. Check completeness. You will need to refine your structure, with an ACTA command in the .ins. After this, open your .cif (type: edit cif in olex) and check the field “_diffrn_measured_fraction_theta_max”. It should be 0.99 or above. If it is lower, you should collect more data, either by a larger wedge, using the mini-kappa (on MX1) or repositioning your crystal and collecting more data on MX2. After this, you will need to merge your data ( CX Data Merging )

Manual data analysis

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 your final cif. For more information on 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

• The XDS processed hkl file for your data processed in P1 without an absorption correction: XDS_ASCII.HKL_P1_NOSCALE

• 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, which includes unit cell information of the data: sad.prp

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

  • 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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• (see above for details)

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

Solving your data

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

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 by typing: shelxt filename (leave off the .ins)

   1. This will give you solved data .res files (most likely in more than one space group), named filename_a.res, filename_b.res etc and some information about the datasets

1. 1. so you can choose which one looks best, or choose the space group which you thought was best based on xprep.

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

   1. shelxle filename_a.res

   2. Olex2 filename_a.res

3. Admire your beautiful structure!

4. Check completeness. You will need to refine your structure, with an ACTA command in the .ins. After this, open your .cif and check the field “_diffrn_measured_fraction_theta_max”. It should be 0.99 or above. If it is lower, you should collect more data, either by a larger wedge, using the mini-kappa (on MX1) or repositioning your crystal and collecting more data. After this, you will need to merge your data ( CX Data Merging )