Topics: Difference between revisions
Jump to navigation
Jump to search
(→Using XDS: add link to PDF) |
|||
| (20 intermediate revisions by 3 users not shown) | |||
| Line 3: | Line 3: | ||
* [[XSCALE]] | * [[XSCALE]] | ||
* [[XDSCONV]] | * [[XDSCONV]] | ||
* [[VIEW]] | * [[VIEW]] (obsolete) | ||
* [[XDS-Viewer]] open-source [[VIEW]] replacement | |||
* [[XDSSTAT]] (this is not part of the XDS package) | * [[XDSSTAT]] (this is not part of the XDS package) | ||
* [[Jiffies]] (little helpful scripts) | * [[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 == | == 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 | |||
* [[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]] | |||
* [[Processing]] | * [[Processing]] | ||
* [[IDXREF]] with subtopics [[Obtaining ORGX ORGY]], [[Ice rings]], [[Reindexing]] | * [[IDXREF]] with subtopics [[Obtaining ORGX ORGY]], [[Ice rings]], [[Indexing]], [[Reindexing]] | ||
* [[CORRECT]], see | * [[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]] | |||
* [https://www.youtube.com/watch?v=XBgqiEXQR-0 Principles of data processing with XDS.] Video recorded at SBGrid/NE-CAT workshop 2014; the PDF is [https://strucbio.biologie.uni-konstanz.de/pub/Principles_of_data_processing_with_XDS.pdf here]. The sound is poor. | |||
== Typical procedures == | == Typical procedures == | ||
* [[Space group determination]], see also [[Reindexing]] | * [[Space group determination]], see also [[Reindexing]] and [[Indexing]] | ||
* [[Optimization]], subtopics [[MINIMUM_ZETA]], [[Aliens]], see also [[Ice rings]] | * [[Optimization]], subtopics [[MINIMUM_ZETA]], [[Aliens]], see also [[Ice rings]] | ||
* [[Determining VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS]] | * [[Determining VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS]] | ||
| Line 21: | Line 34: | ||
== XDS development == | == XDS development == | ||
* [[INTEGRATE]] - how does INTEGRATE work? | |||
* [[Quality Control]] | * [[Quality Control]] | ||
* [[Known Bugs]] | * [[Known Bugs]] | ||
* [[Wishlist]] | * [[Wishlist]] | ||
* [[Features that are not officially documented]] | * [[Features that are not officially documented]] | ||
== external Links == | |||
* [https://xia2.github.io/ xia2] Automated Data Reduction | |||
Latest revision as of 19:21, 15 June 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 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