Processing data with XDS

We’ve made XDS available on both graphics1 and delphi.

Your data will typically be in /data/username

Please do NOT process your data in the /data directory.

please create a parallel directory in /home

For example if your data is in /data/classen/lysozyme/wedge1 then process your data in /home/classen/lysozyme/wedge1.

XDS binaries are available in /programs/xds64/

If you are familiar with XDS and have a favorite XDS.INP file then that’s probably all you need to know.

If you are new to XDS, I would highly recommend browsing the XDS wiki and for detailed explanation of the XDS keywords and program options then look at the official documentation pages. If you would like to run a quick script that will run three rounds of integration and scaling then run this script in your parallel /home directory

generate_XDS.INP "/data/classen/lysozyme/wedge1/xta1_1_00???.img"

The “???.img” is a wildcard selector to indicate all frames between 001 and 999. If you just want to process the first 10 frames then use just two “?“s

The generate_XDS.INP script will produce an XDP.INP that you can further customize in order to fine tune the processing of your data. The XDS wiki has some examples of processing multiple wedges of data and scaling them together as well as some tips and tricks for processing MAD/SAD data expected to have an anomolous signal.

Type xds_par to run the parallel processor version of XDS (It’s very fast…. use it.)

After the xds_par is finished there will be integrated and scaled HKL files (XDS_ASCII.HKL) and various log files, the all important CORRECT.LP log file. This has all your info regarding scaling statistics.

Seriously, this is a great program and easy to use. If you’d like a walk through your first XDS session just drop me a line.