MRBUMP (CCP4: Supported Program)

NAME

MRBUMP - automated search model generation and automated molecular replacement

SYNOPSIS

mrbump hklin foo_in.mtz seqin foo.seq hklout foo_out.mtz xyzout foo.pdb
[Key-worded input file]

DESCRIPTION

mrbump has three main parts:
  1. Automated search for molecular replacement search models for a target structure.
  2. Preparation of these template models for molecular replacement using several different methods.
  3. Running molecular replacement using these search models and testing whether the resulting solutions will refine.
Note that mrbump relies heavily on making calls to web-based applications. If your sequence information is any way sensitive it is recommended that you use the option to run the fasta search locally rather than via the OCA web application. This will require installing fasta34 on the users local machine. The software can be downloaded from the EBI website here.

DEPENDENCIES

Before mrbump can be used, the following dependencies should be installed on the local system. mrbump also requires that the local machine has a connection to the internet (directly or via a proxy).

INPUT AND OUTPUT FILES

HKLIN

Input structure factor file for target structure. Must include a FreeR_flag column.

SEQIN

Input sequence file for the target structure. Can be in PIR or Fasta format or it can just contain the amino acid sequence.

HKLOUT

MTZ file from Refmac5 refinement of the top MR solution.

XYZOUT

PDB coordinate file from Refmac5 refinement of the top MR solution.

KEYWORDED INPUT

LABIN <program label>=<file label>...

Mandatory. This keyword tells the program which columns in the MTZ file should be used as native structure factors, sigmas, and FreeR flag. Available program labels are F, SIGF and FreeR_flag.

JOBID <job name>

Mandatory. This is a name for the job. A directory called "search_JOBID" will be created in the directory in which mrbump is started from. This directory will contain all of the downloaded files and results.

ROOTDIR <directory>

The root directory where the search folder will be created.
[Default Current working directory]

NMASU <number>

The number of molecules in the a.s.u. If this is not specified the value willl be calculated automatically using the Matthews Coefficient.

MDLNUM <number>

The number of template models to be prepared for molecular replacement.
[Default 50]

MRNUM <number>

The number of prepared models to be used molecular replacement.
[Default 20]

ENSEMNUM <number>

The number of prepared models to be used in a Phaser Ensemble.
[Default 5]

IGNORE <pdb id 1> <pdb id 2>...

A list of PDB ID codes to be ignored in the homologue search. Used for development purposes.

INCLUDE <chain id 1> <chain id 2>...

A list of Chain ID codes to be included in the homologue search. Chains must be specified in the format "PDBID_ChainID" e.g. 1nio_A. Used for development purposes.

MRPROGRAM [ Amore | Molrep | Phaser ]

Name of the molecular replacement program to be used as the first.
[Default Molrep]

MAPROGRAM [ Mafft | Clustalw ]

Name of the sequence alignment program to be used to do multiple alignment of the template structure sequences and the target structure sequence.
[Default Mafft]

PACK <number>

Specifies the PACK keyword for Phaser. This is the number of clashes that will be tolerated by Phaser.
[Default 5]

DEBUG [ True | False ]

If true will mrbump will give a more verbose output. Also, temporary directories will not be deleted at the end of the job.
[Default False]

SSMSEARCH [ True | False ]

If true mrbump will use the top match from the sequence-based search in a secondary structure-based search to find more potential homologues. Set to false by default. Requires perl and the perl SOAP-Lite module to be installed.
[Default False]

SCOPSEARCH [ True | False ]

If true mrbump will use the SCOP database to look for individual domains in the template structures found in the sequence-based and secondary structure-based searches.
[Default True]

PQSSEARCH [ True | False ]

If true mrbump will use the PQS service at the EBI to find more multimers based on the template structures found in the sequence-based and secondary structure-based searches.
[Default True]

PWALIGN [ True | False ]

If true, mrbump will generate pair-wise alignments between the target sequence and template sequences in addition to those generated by the multiple alignment. This gives and additional set of search models prepared by Chainsaw. Mainly for development purposes.
[Default False]

FASTALOCAL [ True | False ]

If true, the fasta sequence-based search will be carried out locally rather than via the OCA web-interface. This requires that the user have fasta34 installed on there system. This can be downloaded from the EBI site here.
[Default False]

RUNLOCAL [ True | False ]

If true, the searches will be carried out using the locally installed databases. A network connection will still be required for downloading PDB files. The SSM and PQS searches are turneed off in this case.
[Default False]

CLUSTER [ True | False ]

If true, the model preparation and molecular replacement jobs will be farmed out to a cluster. Currently only works for Sun Grid Engine enabled clusters.
[Default False]

END

End keyworded input.

EXAMPLE KEYWORD INPUT FILES

Simple example with minimal input using default values: 

LABIN F=F SIGF=SIGF FreeR_flag=FreeR_flag
JOBID MY_JOB_1

A more elaborate example: 

LABIN F=FP SIGF=SIGFP FreeR_flag=FREE
JOBID MY_JOB_2
MDLNUM 20
MRNUM 10
ENSEMNUM 5
IGNORE 1smw 1smm 1smu
MRPROGRAM molrep
MAPROGRAM mafft
DEBUG true
CLUSTER false 
SCOPSEARCH true
SSMSEARCH true
PQSSEARCH true
END

PROGRAM OUTPUT

Once a job has been started a user may view the current status of the job via the output log file or via the results.html web page which is created in the directory <ROOTDIR>/search_<JOBID>/results and is updated after each stage in the process. A set of search models is first generated and these are fed to the MR/refinement stage in sequence where the ordering depends on the alignment score of the template sequence against the target sequence. If a suitable solution is found, i.e. a model that refines well, the job will terminate and the final results will be displayed. The resulting refined PDB model and MTZ output from Refmac are made available to the user for further model building.

AUTHORS

Ronan Keegan, Daresbury Laboratory, UK,
Martyn Winn, Daresbury Laboratory, UK

ACKNOWLEDGEMENTS

Norman Stein, Pryank Patel.

List of programs used

pdbset
pdbcur
coord_format
superpose
chainsaw
molrep
phaser
refmac5