Spot2pdb

From XDSwiki

spot2pdb,[1] is a jiffy that creates pseudo-PDB files for visualization of reciprocal space, based on SPOT.XDS and XPARM.XDS. The "atom" positions in the pseudo-PDB files are actually reflections positions in reciprocal space.

The usage is simple: just run

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).

By default, the program creates pseudo-PDB files with reflections up to 6Å. The maximum resolution can be adjusted with the -r option.

Visualization can then be achieved with

coot SPOT-*.pdb

Since there exist duplicate residue numbers in SPOT-indexed.pdb, one needs a ~/.coot with the line

(allow-duplicate-sequence-numbers)

Even better visualization of the raw data and their abstraction as reflection positions is achieved with

coot --pdb SPOT-*.pdb --map rs_mapper_output.ccp4

provided that dials.rs_mapper is run beforehand. The latter is as easy as

dials.rs_mapper /path/to/reflection/files.ext

and produces a CCP4 map file with pixel contents mapped to reciprocal space, to 6Å.


Examples

Indexed spot positions are yellow, un-indexed ones red.
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 Notes below).


Examples with wrong ROTATION_AXIS:

ROTATION_AXIS is -1 0 0 instead of 1 0 0
another view of result with rotation axis backwards
ROTATION_AXIS is 0 1 0 instead of 1 0 0
another view of result with rotation axis 90° off


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.
  • Since dials.rs_mapper uses the STARTING_ANGLE information from the frame headers, the mappings can only agree if XDS.INP also has this item. generate_XDS.INP versions since 0.82 write XDS.INP with STARTING_ANGLE information; earlier versions don't.
  • if no XPARM.XDS exists, one may use XDS.INP as a source of geometry information for spot2pdb.
  • coot 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 coot's display objects (Paul Emsley, personal communication).