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.
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.
The root directory where the search folder will be created.
[Default Current working directory]
The number of molecules in the asymmetric unit. Leave this blank for automatic calculation.
[Default Automatic]
The number of template models to be prepared for molecular replacement.
[Default 50]
The number of prepared models to be used molecular replacement.
[Default 20]
The number of prepared models to be used in a Phaser Ensemble.
[Default 5]
A list of PDB ID codes to be ignored in the homologue search. Used for development purposes.
Names of Molecular Replacement programs to try search models in. Options are Molrep, Phaser or both.
If both are selected Molrep will be used first.
[Default Molrep]
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]
If true models will be prepared for MR using the PDBclip method. With this method, the waters and hydrogens
are removed from the coordinate file and the most probable side-chain confirmations are selected. If chain ID's
are missing they are added.
[Default True]
If true Polyalanine models will be prepared for the MR step. All side-chains are removed from the PDB files.
[Default True]
If true models will be prepared using Molrep. Molrep does a sequence alignment of the target sequence and
the template sequence and prunes the template structure file accordingly.
[Default True]
If true models will be prepared using Chainsaw. Chainsaw takes in a sequence alignment of the target sequence and
the template sequence and prunes the template structure file accordingly.
[Default True]
If true mrbump will give a more verbose output. Also, temporary directories will not be
deleted at the end of the job.
[Default 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]
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]
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]
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]
The number of clashes that Phaser will tolerate.
[Default 5]
The number of cycles of restrained refinement to use in Refmac.
[Default 30]
If true, the search database files will be tested at the start of the job to see if they are out of date
with respect to those available from the EBI website. If they are found to be out of date, the latest version
will be downloaded.
[Default True]
If true, only the search models will be generated. The program will exit before any Molecular Replacement
is carried out.
[Default False]
If true, the program will try all of the search models in molecular replacement. If false the program will
exit when it finds the first solution.
[Default False]
If true, the program will write out a html format summary of the results as they are generated. Requires
that gnuplot is installed to generate plots.
[Default 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]
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 |
Norman Stein, Pryank Patel.
Any publication arising from use of MrBUMP should include the following reference:
R.M.Keegan and M.D.Winn (2006) in preparation
In addition, authors of specific programs should be referenced where applicable: