BUCCANEER (CCP4: Supported Program)

NAME

buccaneer - Statistical protein chain tracing

SYNOPSIS

cbuccaneer -title title -mtzin filename -seqin filename -pdbin filename -pdbin-mr filename -pdbin-sequence-prior filename -pdbout colpath -colin-fo colpath -colin-hl colpath -colin-phifom colpath -colin-fc colpath -colin-free colpath -resolution resolution -find -grow -join -link -sequence -correct -filter -ncsbuild -prune -rebuild -fast -anisotropy-correction -build-semet -fix-position -cycles number of cycles -fragments number of fragments -fragments-per-100-residues number of fragments -ramachandran-filter type -main-chain-likelihood-radius radius/A -side-chain-likelihood-radius radius/A -sequence-reliability reliability -new-residue-name type -new-residue-type type -correlation-mode -known-structure known-structure-spec -jobs -mtzin-ref filename -pdbin-ref filename -colin-ref-fo colpath -colin-ref-hl colpath -verbose verbosity -stdin
[Keyworded input]

DESCRIPTION

'buccaneer' performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target.

The target distributions 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 default 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.

The calculation involves 10 stages:

Finding C-alphas

Candidate C-alpha positions are located by searching the electron density.

Growing fragments

The candidate C-alphas or input chains are grown by adding residues at either end, according to the density.

Joining Fragments

Overlapping fragments are joined to make longer chains. If this leads to a junction in a chain, the contested residue is removed.

Linking Fragments

Nearby N and C termini are examined to see if they can be linked by a short loop.

Assigning Sequence

Likelihood comarison between the density of each residue in the work structure and the residues of the reference structure allows sequence to be assigned to longer fragments.

Correcting sequence.

Insertions and deletions in the model building are fixed by rebuilding, where possible.

Filtering fragments in poor density

Residues in poor density are removed.

Building NCS

Any NCS relationships found in the model are used to augment the related chains.

Pruning Fragments

Clashing fragments are examined and the one with the worse density is removed. This stage can be disabled by the -no-prune keyword.

Rebuilding

Rebuilding allows side chain atoms and carbonyl oxygens to be rebuilt.

INPUT/OUTPUT FILES

-mtzin

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

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

-pdbin

[Optional] Input PDB file containing an initial model to extend.

-pdbin-mr

[Optional] Input PDB file containing an MR model to augemnt the output model. (It is not clear if this option is worthwhile.)

-pdbin-sequence-prior

[Optional] Input PDB file containing an model containing heavy atoms or known residues to help with sequencing.

-pdbout

[Optional] Output PDB file. This will contain the new chain trace.

-pdbin-ref

[Optional] Input PDB file containing the final model for the reference structure.

-mtzin-ref

[Optional] 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.

KEYWORDED INPUT

-colin-fo colpath

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

-colin-hl colpath

Hendrickson-Lattman coefficients for work structure. Either -colin-hl or -colin-phifom should be specified, but not both. See Note on column paths.

-colin-phifom colpath

Phase and figure of merit for work structure. Either -colin-hl or -colin-phifom should be specified, but not both. See Note on column paths.

-colin-fc colpath

[Optional] Initial map coefficients (F and phase) for work structure. These must be on the same scale as the observed F's (i.e. do not use after phaser or phenix.refine). See Note on column paths.

-resolution resolution/A

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

-find

[Optional] Enable growing of fragments.

-grow

[Optional] Enable growing of fragments.

-join

[Optional] Enable joining of fragments.

-link

[Optional] Enable linking of nearby fragments.

-sequence

[Optional] Enable sequencing of fragments.

-correct

[Optional] Enable correction of any missing or extra residues uncovered during the sequencing process.

-filter

[Optional] Enable removal of residues in low density or linking disjoint sequence.

-ncsbuild

[Optional] Enable use of NCS to build related molecules, if present.

-prune

[Optional] Enable pruning of fragments.

-rebuild

[Optional] Enable rebuilding of side-chains and Carbonyl Oxygens.

-fast

[Optional] Use fastest rather than best methods. Typically gives 2-3x speedup for a very similar model, but results vary.

-anisotropy-correction

[Optional] Correct the input F's for anisotropy.

-build-semet

[Optional] Build MSE instead of MET for selenomethionine experiments.

-fix-position

[Optional] Build new model in the same place in the unit cell as the input model.

-cycles number of cycles

[Optional] Number of cycles of building to run. Running multiple cycles leads to a more complete model, although it is not as effective as recycling with refmac.

-fragments number of fragments

[Optional] Maximum number of fragments to build.

-fragments-per-100-residues number of fragments

[Optional] Approximate number of fragments to build per 100 residues (assuming average solvent).

-ramachandran-filter type

[Optional] Only use particular types of residues when preparing the main chain likelihood search function. By selecting particular secondary structure types, it is possible to prefferentially find different types of sequence. type may be one of all, helix, strand, nonhelix.

-main-chain-likelihood-radius radius/A

[Optional] Default 4.0A. For very low resolution maps it may be worth increasing this.

-side-chain-likelihood-radius radius/A

[Optional] Default 5.5A.

-sequence-reliability reliability

[Optional] Values between 0.5 and 1.0 vary the relibility cutoff for docking a sequence. The value is the probability at which the sequence will be accepted. 0.5 means every sequence will be docked, 1.0 means that no sequences are docked. Default = 0.95.

-new-residue-name type

[Optional] Set the name which will be given to newly built residues.

-new-residue-type type

[Optional] Set the type of residue to be used when building new residues.

-correlation-mode

[Optional] Use the correlation target function for growing new chains and for sequencing. This is less effective for initial building, but better for model completion, especial after molecular replacement.

-known-structure known-structure-spec

A single known-structure group can be specified in the general parameters (above), however for more complex cases multiple groups can be defined using keyword input. The known-structure keyword allows atoms or chains from the input model (given using the 'Specify input model to be extended' button at the top of the window) to be preserved. This can be useful when heavy atoms or nucleotide chains comprise a significant portion of the scattering.

Syntax: known-structure coordinateID:radius

Atoms specified by the coordinateID will be retained in the output structure. If a radius is specified, then no main chain atoms will be built within the given radius of the specified atoms. Multiple known-structure keywords may be given with different radii. Examples:

• known-structure /A/*/*/:2.0

Keep all atoms in the A chain and don't build within 2A.

• known-structure /*/*/ZN  /:3.0

Keep all Zinc atoms and don't build within 3A.

• known-structure //*/*/

Keep all atoms in the unlabelled chain.

-jobs CPUs

[Optional] Set number of CPUs to use.

-colin-ref-fo colpath

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

-colin-ref-hl colpath

[Optional] 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.

-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 traditional non-grouped columns from existing files by giving a comma-separated list of names, e.g. 'FP,SIGFP' or 'HLA,HLB,HLC,HLD'.

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 number of residues sequenced and the Free-R factor from refmac are the most useful outputs. These may easily be found using the 'Annotated log file'.

Problems:

AUTHOR

Kevin Cowtan, York.

SEE ALSO