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Spot2pdb: Difference between revisions
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[ | [https://{{SERVERNAME}}/pub/linux_bin/spot2pdb spot2pdb],[https://{{SERVERNAME}}/pub/sources/spot2pdb.f90] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on <code>SPOT.XDS</code> and <code>XPARM.XDS</code>. The "atom" positions in the pseudo-PDB files are actually reflections positions in reciprocal space. | ||
The usage is simple: just run | The usage is simple: just run | ||
spot2pdb | spot2pdb | ||
in a XDS directory containing SPOT.XDS and XPARM.XDS . The program then creates SPOT-indexed.pdb and SPOT-notindexed.pdb, depending on whether SPOT.XDS has indices attached to spot positions or not (or just 0 0 0). Thus it is useful directly after COLSPOT, but even more after IDXREF. Reflections of SPOT-indexed.pdb can be clicked, and have (atomname residuename sequencenumber) corresponding to (H K L). | in a XDS directory containing <code>SPOT.XDS</code> and <code>XPARM.XDS</code>. The program then creates <code>SPOT-indexed.pdb</code> and <code>SPOT-notindexed.pdb</code>, depending on whether <code>SPOT.XDS</code> has indices attached to spot positions or not (or just 0 0 0). Thus it is useful directly after COLSPOT, but even more after IDXREF. Reflections of <code>SPOT-indexed.pdb</code> can be clicked, and have (atomname residuename sequencenumber) corresponding to (H K L). | ||
By default, the program creates pseudo-PDB files with reflections up to 6Å. The maximum resolution can be adjusted with the -r option. | By default, the program creates pseudo-PDB files with reflections up to 6Å. The maximum resolution can be adjusted with the -r option. | ||
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Visualization can then be achieved with | Visualization can then be achieved with | ||
coot SPOT-*.pdb | coot SPOT-*.pdb | ||
'''Since there exist duplicate residue numbers in SPOT-indexed.pdb, one needs a ~/.coot with the line | '''Since there exist duplicate residue numbers in <code>SPOT-indexed.pdb</code>, one needs a <code>~/.coot</code> with the line | ||
(allow-duplicate-sequence-numbers)''' | (allow-duplicate-sequence-numbers)''' | ||
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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: | |||
* the mapping used by dials.rs_mapper uses the (unrefined) frame header values, and possibly assumptions (as implemented in iotbx.detectors) 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. | == Examples == | ||
* if no XPARM.XDS exists, | [[File:insu6A.png|400px|thumb|left|Indexed spot positions are yellow, un-indexed ones red.]] | ||
[[File:insu6AplusED.png|400px|thumb|right|Same, but with pseudo electron density. The offset between spot positions and electron density is due to a slight error in the header values of ORGX, ORGY (see [[spot2pdb#Notes|Notes]] below).]] | |||
<br clear=all>Examples with wrong ROTATION_AXIS: | |||
[[File:backwardsrotaxis.png|400px|thumb|left|ROTATION_AXIS is -1 0 0 instead of 1 0 0]] | |||
[[File:backwardsrotaxis2.png|400px|thumb|right|another view of result with rotation axis backwards]] | |||
[[File:wrongrotaxis.png|400px|thumb|left|ROTATION_AXIS is 0 1 0 instead of 1 0 0]] | |||
[[File:wrongrotaxis2.png|400px|thumb|right|another view of result with rotation axis 90° off]] | |||
<br clear=all> | |||
== 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. | |||
* 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 for most detectors. | |||
* if no <code>XPARM.XDS</code> exists, spot2pdb uses [https://{{SERVERNAME}}/pub/linux_bin/generate_XPARM.XDS XDS.INP as a source of geometry information]. | |||
* <code>coot</code> connects atoms that are close, have residue numbers differing by at most 1, and are in the same chain, with bonds (lines) (Paul Emsley, personal communication). 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'' (Paul Emsley, personal communication). | |||