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Tutorial(First Steps): Difference between revisions
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→A beginner's walk-through to XDS: update
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This tutorial is directed at people who are beginners to XDS and do not want to start reading about all the technical details but rather want their images processed. Other processing programs are often more attractive to new users because using a GUI make starting easier than a [[XDS.INP|script file]]. If you notice a mistake or gap in this tutorial, please contact the authors. | This tutorial is directed at people who are beginners to XDS and do not want to start reading about all the technical details but rather want their images processed. Other processing programs are often more attractive to new users because using a GUI make starting easier than a [[XDS.INP|script file]]. If you notice a mistake or gap in this tutorial, please contact the authors. | ||
In the following, the manual mode of setting up XDS.INP is explained. | In the following, the manual mode of setting up [[XDS.INP]] and running XDS is explained. | ||
There is also a [[generate_XDS.INP|script]] that sets up XDS.INP automatically, at least for common types of detectors. Much easier than setting up and running XDS manually should be the usage of [[XDSGUI]]. | |||
== Setting up == | == Setting up == | ||
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It is not recommended to process the images from within the same directory as the images are. At least create a subdirectory. In many cases the data images are on an external disk or remotely mounted directory with an awfully long path name. | It is not recommended to process the images from within the same directory as the images are. At least create a subdirectory. In many cases the data images are on an external disk or remotely mounted directory with an awfully long path name. | ||
If | If your images are at a path with embedded blanks, e.g. "/my/USB disk/path", XDS is not able to access the images and one must create a link to the actual directory: | ||
#> ln -s "/my/USB disk/path" images | |||
=== Getting [[XDS.INP]] === | === Getting [[XDS.INP]] === | ||
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Then data processing can start. type <pre>#> xds_par </pre> to run xds and wait until it's finished. | Then data processing can start. type <pre>#> xds_par </pre> to run xds and wait until it's finished. | ||
== Indexing Fails == | == Indexing Fails == | ||
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If it deviates by more than 1-2mm from the input distance, check all your parameters again. Is the wavelength really correct, as well as the distance? If you are sure about them, try indexing with only a few images | If it deviates by more than 1-2mm from the input distance, check all your parameters again. Is the wavelength really correct, as well as the distance? If you are sure about them, try indexing with only a few images | ||
SPOT_RANGE = 1 20 | SPOT_RANGE = 1 20 | ||
== See also == | |||
[https://{{SERVERNAME}}/pub/MWhitley_CSHL-2018_XDS-Tutorial.pdf Matthew J. Whitley's excellent tutorial] about XDS processing with [[XDSGUI]], from the 2018 Cold Spring Harbor X-Ray Methods in Structural Biology Course. | |||