Topics: Difference between revisions
Jump to navigation
Jump to search
| (3 intermediate revisions by the same user not shown) | |||
| Line 12: | Line 12: | ||
== Using XDS == | == Using XDS == | ||
* [https://www.youtube.com/watch?v=3WU9NrILECo XDS and XDSGUI. SBGrid Webinar by Kay Diederichs, May 2020] [https://strucbio.biologie.uni-konstanz.de/pub/Crystallographic_data_processing_with_XDS_using_XDSGUI.pdf slides of the talk] | |||
* [[XDS.INP]] | * [[XDS.INP]] | ||
* [[generate_XDS.INP]] - quick procedure to obtain XDS.INP for MarCCD, ADSC, Pilatus detectors | * [[generate_XDS.INP]] - quick procedure to obtain XDS.INP for MarCCD, ADSC, Pilatus, ... detectors | ||
* [[Tutorial(First_Steps)|Tutorial]] Quick beginner's walk-through if you just want to get going. | * [[Tutorial(First_Steps)|Tutorial]] Quick beginner's walk-through if you just want to get going. | ||
* [https://{{SERVERNAME}}/pub/MWhitley_CSHL-2018_XDS-Tutorial.pdf Matthew J. Whitley's excellent tutorial] about XDS processing with [[XDSGUI]], from the 2018 CSHL X-Ray Methods in Structural Biology Course. | |||
* [[FAQ]] | * [[FAQ]] | ||
* [[Processing]] | * [[Processing]] | ||
| Line 22: | Line 24: | ||
* worked-out '''examples''': see in particular the five projects ([[2QVO]], [[3CSL]], [[simulated-1g1c]], [[1Y13]] and [[2VB1]]) at the bottom of [[Quality Control]]. | * worked-out '''examples''': see in particular the five projects ([[2QVO]], [[3CSL]], [[simulated-1g1c]], [[1Y13]] and [[2VB1]]) at the bottom of [[Quality Control]]. | ||
* [[XDSGUI]] | * [[XDSGUI]] | ||
* [https://www.youtube.com/watch?v=XBgqiEXQR-0 Principles of data processing with XDS.] Video recorded at SBGrid/NE-CAT workshop 2014. The sound is poor. | |||
== Typical procedures == | == Typical procedures == | ||
| Line 39: | Line 42: | ||
== external Links == | == external Links == | ||
* [ | * [https://xia2.github.io/ xia2] Automated Data Reduction | ||
Revision as of 18:46, 8 May 2020
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 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