Running shift-field refinement

Example for coordinate only The following command and keywords will run shift-field coordinate refinement on the input model. The resulting model of the refinement will have the default filename of shiftfield_refined_final.pdb. A log file (pysheetbend.log) will be written at the end.

$ pysheetbend refine_model_to_map2 --mapin MAP_PATH \
  --pdbin PDB_PATH --radius-scale 4.0 \
  --resolution RESOLUTION --res-by-cyc 6.0 3.0 \
  --cycle 12 --macro-cycles 3 --coord \
  --pseudo-regularise postref

  • --radius-scale is the scale factor to calculate the radius value from the resolution

  • --resolution is the resolution of the map

  • --res-by-cycle is the starting and ending or list of resolutions for refinement. If ending resolution given is higher than –resolution, then the value from –resolution will be used as ending resolution.

  • --cycles is the number of refinement cycles within each resolution cycle.

  • --macro-cycles is the number of refinement cycles. The refinement resolution changes in each macro cycle.

  • --coord to turn on coordinate refinement

  • --pseudo-regularise postref is to pseudo-regularise the model at the end of each macro cycle. Other options are yes to pseudo-regularise the model every cycle, or no for none.

Example for B-values only The following command and keywords will run shift-field atomic B-value refinement on the input model. The resulting model of the refinement will have the default filename of shiftfield_refined_final.pdb. A log file (pysheetbend.log) will be written at the end.

$ pysheetbend refine_model_to_map2 --mapin MAP_PATH \
  --pdbin PDB_PATH --radius-scale 4.0 \
  --resolution RESOLUTION --res-by-cyc 6.0 3.0 \
  --macro-cycles 3 --uiso

  • --radius-scale is the scale factor to calculate the radius value from the resolution

  • --resolution is the resolution of the map

  • --res-by-cycle is the starting and ending or list of resolutions for refinement. If ending resolution given is higher than –resolution, then the value from –resolution will be used as ending resolution.

  • --macro-cycles is the number of refinement cycles. The refinement resolution changes in each macro cycle.

  • --uiso to turn on B-value refinement

Keyworded input:

Input files and related keywords

  • --mapin Input map file

  • --pdbin Input PDB/mmCIF file containing the model to be refined

  • --maskin [optional] Input mask.

  • --nomask [optional] Do not mask input map. If specified, program will not mask input map for refinement.

  • --no-ligands [optional] Remove ligands. If specified, ligands will not be read from input file.

  • --no-waters [optional] Remove waters. If specified, waters will not be read from input file.

Output files and related keywords

  • --pdbout [optional] Output filename. Will use the given filename as prefix to the final output filename. Default: shiftfield.pdb

  • --xmlout [optional] XML filename. Default: program.xml

  • --no-xmlout [optional] Do not write XML output. If specified no XML output will be written.

  • --intermediate [optional] Output model files every cycle.

Refinement parameters

  • --resolution Resolution of the input map. This value will be used to calculate values of sample rate and grid spacing used for calculating resampling grids. If res-by-cycle is not given, refinement will run at this resolution only.

  • --res-by-cycle Set the resolution for each macro cycle. Resolutions are separated by space. If there are fewer resolutions than macro-cycles, linear interpolation is used to fill in the remaining values.

  • --cycles Number of cycles within each resolution/macro cycle. Default: 1

  • --macro-cycles Number of resolution/macro cycles. Default: 1

  • --radius Set the radius to be used in shift-field refinement. This controls the size of the regions which are ‘dragged’ by the morphing calculation. Larger radii lead to bulkier changes, smaller radii allow smaller features to move independently, at a cost of messing up the geometry. Avoid radius < 2.5*resolution. Default = radius_scale*resolution of the cycle

  • --radius-scale Set the radius in proportion to the resolution for the current cycle. The resolution is multiplied by this factor to get the radius. Overidden by radius.

  • --coord Performs coordinate refinement. If not refinement option is specified, coordinate refinement is enabled by default.

  • --uiso Performs B-factor refinement.

  • --pseudo-regularise Pseudo-regularise the model. Default = postref. no: turn off pseudo-regularise. yes: run at the end of every cycle. postref: run only at the end of every macro cycle.

  • --b-iso-range Set the lower and upper bound of B-isotropic value refinement. Separated by space.

Miscellaneous

  • --verbose Set verbosity of the terminal output.