SLOOP (CCP4: Unsupported Program)

NAME

sloop - Loop building

SYNOPSIS

csloop -pdbin filename -mapin filename -mtzin filename -pdbout filename -pdbout-loops filename -colin-fo colpath -colin-hl colpath -colin-fc colpath -colin-free colpath -resolution resolution/A -clash-radius radius/A -clash-penalty penalty -protein-db filename -verbose verbosity -stdin
[Keyworded input]

DESCRIPTION

'sloop' performs loop building by finding gaps in the chain and using fragments from the Richardson's Top500 library of structures to fill the gaps.

'sloop' is a temporary testbed program. If it is successful the functionality will eventually be incorporated into 'coot'.

HOW TO RUN SLOOP

A PDB file and some source of electron density are required - the latter can be in the form of an electron density map, or an MTZ file containing phase information. Gaps will be identified in the PDB file where there is a jump in sequence numbering within a chain. The number of residues inserted will depend on the sequence numbering.

The calculation is very fast, and the time taken is independent of the loop size. However, as the loops get bigger the chance of finding a good fit drops. There is a maximum limit of 16AA, although in practice it is unlikely to be useful for loops of more that 8AA.

Examples

csloop --pdbin my.pdb --mapin my.map

csloop --pdbin my.pdb --mtzin my.mtz --colin-fc FWT,PHWT

csloop --pdbin my.pdb --mtzin my.mtz --colin-fo FP,SIGFP --colin-hl HLADM,HLBDM,HLCDM,HLDDM

INPUT/OUTPUT FILES

-pdbin

Input PDB file containing the model to be completed.

-mapin

Input electron density map. Either a map or mtz file must be supplied

-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 containing the completed model.

-pdbout-loops

Optional output PDB file name prefix for a set of file, one per chain, containing the best 9 loops found for each position.

-protein-db

Database of binary structures. The file protein.db should have been placed in your ccp4/lib/data directory. If it has not, specify the filename/path with this keyword.

KEYWORDED INPUT

See Note on keyword input.

-colin-fo colpath

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

-colin-hl colpath

[Optional] Hendrickson-Lattman coefficients for work structure. See Note on column paths.

-colin-fc colpath

[Optional] Map coefficients for work structure. See Note on column paths.

-colin-free colpath

[Optional] Free-R flag. See Note on column paths.

-resolution resolution/A

[Optional] Resolution limit for the calculation. All data is truncated.

-clash-radius clash-radius/A

[Optional] Radius below which clashing main chain atoms will be penalised. Default 2.0A.

-clash-penalty clash-penalty

[Optional] Z-score-like penalty to apply for clashing atoms. Default 1.0.

-verbose verbosity

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:

Problems:

AUTHOR

Kevin Cowtan, York.

SEE ALSO