SHEETBEND (CCP4: Unsupported Program)

NAME

sheetbend - Model morphing by shift field refinement

SYNOPSIS

csheetbend -pdbin filename -mtzin filename -pdbout filename -colin-fo colpath -colin-free colpath -cycles cycles -resolution-by-cycle resolution/A,resolution/A,... -coord -u-iso -aniso-obs -aniso-cal -radius-scale scale -radius radius/A -resolution resolution/A -stdin
[Keyworded input]

DESCRIPTION

'sheetbend' performs model morphing by shift field refinement. This is a very fast form of preliminary refinement which can be applied as a precursor to conventional refinement. It can be applied at any resolutions, and when used at low resolution is particularly suited to correcting large shifts in secondary structure elements in molecular replacement. It can also be used to refine B factors.

HOW TO RUN SHEETBEND

A PDB file and a set of structure factors are required. The parameters of the atoms in the PDB file will be updated to better match the observations.

The performance of the calculation is controlled by two parameters, the resolution and the radius - see
   Cowtan, K., & Agirre, J. (2018) Acta Cryst. D74, 125-131.
for details. For coordinate refinement, the calculation would normally start at low resolution (say 6A), and then increase to 3 or 4A before moving to regular refinement. B-value refinement may be usefully performed at higher resolutions, depending on the speed and fit required. The resolution may be set for the whole calculation, or a list of resolutions may be provided describing how the resolution will change over multiple cycles. If the radius is not specified, a default value will be calculated from 4x the resolution.

While little or no optimization has been performed the calculation is already fast, especially when run at low resolutions. Calculation time is dominated by the electron density calculation, which is inefficient by modern standards.

Examples

csheetbend --pdbin my.pdb --mtzin my.mtz --pdbout new.pdb --colin-fo FP,SIGFP -cycles 12 -resolution-by-cycle 6,6,3 

INPUT/OUTPUT FILES

-pdbin
Input PDB file containing the model to be refined.
-mtzin
Input 'work' MTZ file. This contains the data for the unknown, work structure. The required columns are F and phi or F, sigF, and a set of HL coefficients from a phasing, phase improvement, or refinement program.
-pdbout
Output PDB refined the completed model.

KEYWORDED INPUT

See Note on keyword input.

-colin-fo colpath

Observed F and sigma for work structure. See Note on column paths.

-colin-free colpath

[Optional] Free R flag. If provided allows a free-R factor to be calculated. See Note on column paths, Note on free R factors.

-cycles cycles

[Optional] Number of cycles to perform. For coordinates, 10-20 is probably reasonable, B factor refinement is faster. (Default 1)

-resolution-by-cycle resolution/A,resolution/A,...

[Optional] Set the resolution for each cycle of a multi-cycle calculation. Resolutions are specified by a comma separated list of numbers (without spaces). If there are fewer resolutions than cycles, linear interpolation is used to fill in the remaining values.

-coord

[Optional] Perform coordinate refinment. If no refinement option is specified, coordinate refinement is enabled by default.

-u-iso

[Optional] Perform B-factor refinment.

-free-flag flag

[Optional] Free-R set to use. (Default 0)

-aniso-obs

[Optional] Perform anisotropy correction on observed data - currently not recommended. (Default off)

-aniso-obs

[Optional] Perform anisotropy correction on calculated data - currently not recommended. (Default off)

-radius-scale scale

[Optional] Automatically set the radius in proportion to the resolution for the current cycle. The resolution is multiplied by this factor to get the radius. Overridden by 'radius'. (Defauly 4.0)

-radius radius/A

[Optional] Radius of the regression refinement sphere - this controls the size of the regions which are 'dragged' by the morphing calculation. Larger radii lead to bulk changes, smaller radii allow smaller features to move independently, at a cost of messing up the geometry. Avoid radius < 2.5 * resolution.

-resolution resolution/A

[Optional] Resolution limit for the calculation. All data is truncated. If resolutions by cycle are not supplied, this resolution is applied for every cycle. Defaults to the resolution of the MTZ file, which is probably not what you want.

Note on column paths:

When using the command line, MTZ columns are described as groups using a comma separated format. A more specific form includes the crystal and dataset name sparated by slashes, and enclosing any column labels in square brackets. If your data was generated by another column-group using program, you can just specify the name of the group. e.g.
FP,SIGFP
/*/*/[FP,SIGFP]
/native/peak/Fobs
(The last case expands to two column names: Fobs.F_phi.F and Fobs.F_phi.phi)

Note on keyword input:

Keywords may appear on the command line, or by specifying the '-stdin' flag, on standard input. In the latter case, one keyword is given per line and the '-' is optional, and the rest of the line is the argument of that keyword if required, so quoting is not used in this case.

Reading the Ouput:

The program outputs an R-factor (and, if a flag is provided, free R-factor) at the start of each cycle. Note that these are based on the reflections used for a given cycle, which may change if the resolution changes from cycle to cycle. Values are therefore not comparable from cycle to cycle unless the resolution is unchanged. As a result the values are only really useful for evaluating radius settings using the same resolution settings.

The free-R factor is very noisy at low resolutions and degrades performance, so use of a free set is probably inadvisable.

Problems:

AUTHOR

Kevin Cowtan, York.

SEE ALSO