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Spot2pdb: Difference between revisions
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and produces a CCP4 map file with pixel contents mapped to reciprocal space, to 6Å. | and produces a CCP4 map file with pixel contents mapped to reciprocal space, to 6Å. | ||
Notes | |||
== Examples == | |||
[[File:insu6A.png]] | |||
Indexed spot positions are yellow, un-indexed ones red. | |||
[[File:insu6AplusED.png]] | |||
Same, but with pseudo electron density. | |||
== Notes == | |||
* the mapping used by <code>dials.rs_mapper</code> uses the (unrefined) frame header values, and possibly assumptions (as implemented in <code>iotbx.detectors</code>) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree. | * the mapping used by <code>dials.rs_mapper</code> uses the (unrefined) frame header values, and possibly assumptions (as implemented in <code>iotbx.detectors</code>) about geometry aspects, like ROTATION_AXIS, not stored in the header. On the other hand, XPARM.XDS may have different assumptions about geometry aspects, and uses the geometry as refined by IDXREF. Ideally, these two mappings should agree. | ||
* Since <code>dials.rs_mapper</code> uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if <code>XDS.INP</code> also has this item. [[generate_XDS.INP]] versions since 0.82 write <code>XDS.INP</code> with STARTING_ANGLE information; earlier versions don't. | * Since <code>dials.rs_mapper</code> uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if <code>XDS.INP</code> also has this item. [[generate_XDS.INP]] versions since 0.82 write <code>XDS.INP</code> with STARTING_ANGLE information; earlier versions don't. | ||
* if no <code>XPARM.XDS</code> exists, one may use [ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information]. | * if no <code>XPARM.XDS</code> exists, one may use [ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information] for <code>spot2pdb</code>. | ||
* | * <code>coot</coot> connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines). The program makes an attempt to avoid such lines by cycling through chain names; the proper solution would be <code>coot</code>'s ''display objects''. | ||