PARROT (CCP4: Supported Program)

NAME

parrot - Statistical protein chain tracing

SYNOPSIS

cparrot -mtzin-ref filename -pdbin-ref filename -mtzin-wrk filename -seqin-wrk filename -pdbin-wrk-ha filename -pdbin-wrk-mr filename -colin-ref-fo colpath -colin-ref-hl colpath -colin-wrk-fo colpath -colin-wrk-hl colpath -colin-wrk-phifom colpath -colin-wrk-fc colpath -colin-wrk-free colpath -mtzout filename -colout colpath -colout-hl colpath -colout-fc colpath -solvent-flatten -histogram-match -ncs-average -rice-probability -cycles number of cycles -resolution resolution -solvent-content fraction -solvent-mask-filter-radius radius -ncs-mask-filter-radius radius -ncs-asu-fraction fraction -ncs-operator alpha,beta,gamma,x,y,z,x,y,z -verbose verbosity -stdin
[Keyworded input]

DESCRIPTION

'parrot' performs automated density modification, designed as a modern replacement for 'dm'. It uses an evolved traditional algorithm, which means that it runs very quickly, but gives results comparable to statistical density modification programs.

Electron density histograms are generated by a simulation calculation using a known 'reference' structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved, 'work' structure. For almost all cases, a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure.

HOW TO RUN BUCCANEER

A set of reference structure will have been provided with the program. The structure 1TQW is good for typical protein problems at resolutions up to 1.25A, although in practice including data much beyond 2.0A doesn't make much difference. For exotic cases you might want to provide your own reference structures.

INPUT/OUTPUT FILES

-pdbin-ref

Input PDB file containing the final model for the reference structure.

-mtzin-ref

Input 'reference' MTZ file. This contains the data for a known, reference structure. The required columns are F, sigF, and a set of Hendrickson-Lattman (HL) coefficients describing the calculated phases from the final model. Suitable reference structures can be constructed from the PDB using the 'Make Pirate reference' task.

-mtzin-wrk

Input 'work' MTZ file. This contains the data for the unknown, work structure. The required columns are F, sigF, and a set of HL coefficients from phasing improvement.

-seqin-wrk

[Optional] Input sequence file in any common format, e.g. pir, fasta.

-pdbin-wrk-ha

[Optional] Input PDB file containing a heavy atom model, used to determine NCS.

-pdbin-wrk-mr

[Optional] Input PDB file containing a molecular replacement or partially built model, used to determine NCS.

-mtzout

Output MTZ file. This will contain the new HL coefficients and map coefficients.

KEYWORDED INPUT

-colin-ref-fo colpath

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

-colin-ref-hl colpath

Hendrickson-Lattman coefficients for reference structure. If you do not have these, they can be generated using the accompanying chltofom program. See Note on column paths.

-colin-wrk-fo colpath

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

-colin-wrk-hl colpath

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

-resolution resolution/A

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

-cycles number of cycles

[Optional] Number of cycles of density modification to run. 3 or 5 cycles are a good choice if there is no NCS, with NCS more cycles can be used. Too many cycles lead to bias.

-verbose verbosity

Note on column paths:

When using the command line, MTZ columns are described as groups using a slash separated format including the crystal and dataset name. If your data was generated by another column-group using program, you can just specify the name of the group, for example '/native/peak/Fobs'. You can wildcard the crystal and dataset if the file does not contain any duplicate labels, e.g. '/*/*/Fobs'. You can also access individual non-grouped columns from existing files by giving a comma-separated list of names in square brackets, e.g. '/*/*/[FP,SIGFP]'.

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