Topics

Programs

• XDS
• XSCALE
• XDSCONV
• VIEW (obsolete)
• XDS-Viewer open-source VIEW replacement
• XDSSTAT (this is not part of the XDS package)
• Jiffies (little helpful scripts)
• SIM_MX (this is not part of the XDS package)
• adxv (this is not part of the XDS package)
• XDSGUI (this is not part of the XDS package)

Using XDS

• XDS and XDSGUI. SBGrid Webinar by Kay Diederichs, May 2020 slides of the talk
• XDS.INP
• generate_XDS.INP - quick procedure to obtain XDS.INP for MarCCD, ADSC, Pilatus, ... detectors
• Tutorial Quick beginner's walk-through if you just want to get going.
• Matthew J. Whitley's excellent tutorial about XDS processing with XDSGUI, from the 2018 CSHL X-Ray Methods in Structural Biology Course.
• FAQ
• Processing
• IDXREF with subtopics Obtaining ORGX ORGY, Ice rings, Indexing, Reindexing
• CORRECT
• Small molecules how to process difficult datasets, or those with few reflections
• worked-out examples: see in particular the five projects (2QVO, 3CSL, simulated-1g1c, 1Y13 and 2VB1) at the bottom of Quality Control.
• XDSGUI
• Principles of data processing with XDS. Video recorded at SBGrid/NE-CAT workshop 2014; the PDF is here. The sound is poor.

Typical procedures

• Space group determination, see also Reindexing and Indexing
• Optimization, subtopics MINIMUM_ZETA, Aliens, see also Ice rings
• Determining VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS
• Tips and Tricks
• Scaling with SCALA

XDS development

• INTEGRATE - how does INTEGRATE work?
• Quality Control
• Known Bugs
• Wishlist
• Features that are not officially documented

external Links

• xia2 Automated Data Reduction