buccaneer - Statistical protein chain tracing
buccaneer_pipeline.py
-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
-cycles number of cycles
-jobs
-buccaneer-anisotropy-correction
-buccaneer-build-semet
-buccaneer-fix-position
-buccaneer-fast
-buccaneer-new-residue-name
-buccaneer-resolution resolution
-buccaneer-1st-cycles number of cycles
-buccaneer-1st-correlation-mode true/false
-buccaneer-1st-sequence-reliability reliability
-buccaneer-nth-cycles number of cycles
-buccaneer-nth-correlation-mode true/false
-buccaneer-nth-sequence-reliability reliability
-mtzin-ref filename
-pdbin-ref filename
-colin-ref-fo colpath
-colin-ref-hl colpath
-refmac-twin true/false
-refmac-mlhl true/false
-refmac-weight weight
-prefix file/directory name
-verbose verbosity
-buccaneer-keyword keyword
-refmac-keyword keyword
-stdin
[Keyworded input]
'buccaneer' performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. Model building is iterated with refinement in 'refmac' to produce a fairly complete model for use in Coot.
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.
The buccaneer_pipeline program will iterate buccaneer and refmac a
specified number of times, given by -cycles. Each buccaneer run will
involve multiple internal cycles of buccaneer; these may optionally be
specified as well, however the defaults are well chosen. A typical
calculation is therefore as follows:
Cycle Action 1 3 cycles of buccaneer 10 cycles of refmac 2 2 cycles of buccaneer 10 cycles of refmac 3 2 cycles of buccaneer 10 cycles of refmac 4 2 cycles of buccaneer 10 cycles of refmac 5 2 cycles of buccaneer 10 cycles of refmac
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:
-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.
-colin-free colpath
[Optional] Free R flags. See Note on column paths.
-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.
-jobs CPUs
[Optional] Set number of CPUs to use.
-buccaneer-anisotropy-correction
[Optional] Correct the input F's for anisotropy.
-buccaneer-build-semet
[Optional] Build MSE instead of MET for selenomethionine experiments.
-buccaneer-fix-position
[Optional] Build new model in the same place in the unit cell as the input model.
-buccaneer-fast
[Optional] Use fastest rather than best methods. Typically gives 2-3x speedup for a very similar model, but results vary.
-buccaneer-new-residue-name type
[Optional] Set the name which will be given to newly built residues.
-buccaneer-resolution resolution/A
[Optional] Resolution limit for the calculation. All data is truncated.
-buccaneer-1st-cycles cycles
[Optional] Number of internal buccaneer cycles to run on the first iteration. Default 3.
-buccaneer-1st-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. Default false.
-buccaneer-1st-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.
-buccaneer-nth-cycles cycles
[Optional] Number of internal buccaneer cycles to run on subsequent iterations. Default 2.
-buccaneer-nth-correlation-mode
[Optional] As above, for subsequent cycles. Default true.
-buccaneer-nth-sequence-reliability reliability
[Optional] As above, for subsequent cycles. Default = 0.95.
-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.
-refmac-twin true/false
[Optional] Use twin refinement in refmac. Default false.
-refmac-mlhl true/false
[Optional] Use MLHL refinement in refmac. Default true.
-refmac-weight weight
[Optional] Geometry weight to use refmac. Default AUTO.
-prefix file/directory name
[Optional] File prefix or directory name to use for temporary files. If the name ends in a slash, a directory will be created and used. Default buccaneer/.
-verbose verbosity
-buccaneer-keyword keyword
Additional keywords to pass to buccaneer. (Can be repeated.)
-refmac-keyword keyword
Additional keywords to pass to refmac. (Can be repeated.)
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'.
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.
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'.
Kathryn Cowtan, York.