Full model search, model preparation and molecular replacement:
mrbump hklin
foo_in.mtz
seqin
foo.seq
hklout
foo_out.mtz
xyzout
foo.pdb
[Key-worded input]
Model search and preparation only:
mrbump seqin
foo.seq
[Key-worded input]
Molecular replacement only (requires input of output directory of previous run of the program):
mrbump hklin
foo_in.mtz
prepdir
path to previous mrbump job output directory
hklout
foo_out.mtz
xyzout
foo.pdb
[Key-worded input]
MrBUMP has three main parts:
Note that MrBUMP makes a number of calls to web-based applications. If your sequence information is in 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.
Before MrBUMP can be used, the following dependencies should be installed on the local system.
There are a number of options for specifying parameters (e.g. number of molecules expected in the asymmetric unit) or preferences (e.g. which multiple alignment program to use). All options have sensible defaults.
Main keywords:
LABIn, JOBId ROOTdir, RLEVel, NMASu, MRNUm, ENSEmnum, INCLude, LOCAlfile, FIXEd_xyzin, IGNOre, MRPRograms, MAPRogram, MDLDpdbclp, MDLUnmod, MDLPlyala, MDLMolrep, MDLChainsaw, MDLSculptor, SSMSearch, SCOPsearch, PQSSearch, DOFAsta, DOHHpred, DOPHmmer, HHDBpdb, HHSCore, PACK, PJOBS, NCYC, REFTwin, UPDAte, ONLYmodels, TRYAll, USEAcorn, ACORnres, BUCCaneer BCYC ARPWarp ACYC SHELxe SCYC SXREBUILD SXRARPW SXRBUCC USEPHS ENANt
Additional keywords:
PKEYword, PDBDir, PDBLocal, CLUSter, QTYPe, QSIZe, QSUBcom, CLEAn, LITE, PICKle, CHECk, DEBUg, PROXyserver
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.
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]
When performing the homologue search (using Phmmer) what level of redundancy should be used for the
sequence identities. There are currently two options - 70% elimantes all sequences with greater than 70%
identity to each other an 100% which uses all sequences.
[Default 70]
The number of molecules in the asymmetric unit. Leave this blank for automatic calculation.
[Default Automatic]
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 and Chain IDs to be included in the homologue search. Any specific chains
entered here are automatically processed in molecular replacement regardless of how they score in the
template model scoring.
Example: INCLUDE 1nio_A.
Use this keyword to specify the location of a local PDB file to be used as a search model in MrBUMP.
The full path to the file must be specified. The optional CHAIN subkeyword can be used to specify a particular
chain in the PDB file. If CHAIN is not used then the program will extract chain "A" from the file.
Example: LOCALFILE /tmp/1nio.pdb CHAIN A.
The FIXED_XYZIN keyword allows the user to input a fixed component structure in the MR search. This
component should already have the correct orientation. This keyword can be used multiple times if there
are more than one fixed components known. The sequence identity for each component against its corresponding
section of the target sequence is required. The full path to the PDB file should also be specified. Fixed
components are passed to both Phaser and Molrep.
Example: FIXED_XYZIN /tmp/fixed.pdb IDEN 0.43
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 Phaser]
Name of the sequence alignment program to be used to do multiple alignment of the template structure
sequences and the target sequence. In good cases, these programs should give the same result. In
more marginal cases (e.g. small number of sequences, low sequence identity) they may give very
different results.
[Default MAFFT]
If true unmodified search models will be passed to the MR stage. This can be useful when a user is providing
their own pre-prepared search models via the LOCALFILE option.
[Default False]
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 False]
If true Polyalanine models will be prepared for the MR step. All side-chains are removed from the PDB files.
[Default False]
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 models will be prepared using Phaser.Sculptor. Sculptor 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 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, a FASTA search will be carried out to search for the possible template models. A user can turn this
off and give specific chain IDs to be used as the template models. Note that at least one chain must be specified
using the INCLUDE keyword if DOFASTA is set to False. Alterntaively, a local file can be specified with the
LOCALFILE keyword. Requires that fasta34 or fasta35 be installed on the local machine. These are available from
the EBI website: http://www.ebi.ac.uk/fasta.
[Default False]
If true a sequence-based search for template models will be carried out using HHblits from the HHsuite. Using this search
mechanism may give different results from the standard fasta search and produce alternative search models for MR. Note that this
requires that the user has installed the hhsuite separately along with it's associated pdb sequence database. If this keyword is
set to true the user must also specify the path to the hhsuite pdb database file using the HHDBpdb keyword
and the hhsuite uniprot database index file using the HHINdex keyword. In addition the
HHLIB environment variable must be set to point to the hhsuite "lib/hh" directory (see hhsuite setup instructions for details).
The HHsuite can be downloaded from: http://toolkit.tuebingen.mpg.de/hhpred.
[Default False]
If true, a phmmer sequence-based search will be carried out to search for the possible template models. [Default True]
Use this keyword to specify a directory where MrBUMP can find the HHsuite PDB sequence database files.
This keyword is required if the user wishes to use the hhpred suite to search for template models. It is only
needed if the DOHHpred keyword is set to "True". It should give the full path to the hhsuite pdb70 database directory
followed by the base name for the pdb sequence file e.g. "HHDBPDB /usr/local/hhsuite/database/pdb70/pdb70_08Feb14_hhm_db"
[Default Not set]
Use this keyword to specify a directory where MrBUMP can find the HHsuite uniprot sequence database index file.
This keyword is required if the user wishes to use the hhpred suite to search for template models. It is only
needed if the DOHHpred keyword is set to "True". It should give the full path to the hhsuite uniprot database index file
e.g. "HHINDEX /usr/local/hhsuite/database/uniprot20/uniprot20_hhm_db.index"
[Default Not set]
If DOHHPRED is true this keyword, when true, instructs MrBUMP to use the alignments generated in the HHblits sequence search for templates
as the alignments used to score the template models (only for templates found by the HHblits search). In addition, both Sculptor and Chainsaw
will be given the HHblits alignments for search model preparation. If set to false the alignments generated using the selected multiple alignment
program (e.g. MAFFT) will be used for the scoring of template models.
[Default True]
The number of clashes that Phaser will tolerate.
[Default 5]
The number of processing cores that Phaser will will use in parallel. Note that when the CLUSTER keyword is set to True (molecular replacement jobs submitted to a cluster queue) PJOBS is always set to 1.
[Default 2]
The number of cycles of restrained refinement to use in Refmac.
[Default 30]
Set this keyword to true if the indications are that your data is twinned. The "TWIN" keyword will be used in
Refmac which will determine and account for the twinning in refinement. Only valid for Refmac version 5.5 or later.
[Default False]
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, program will put each positioned and refined search model through the program Acorn to try and improve the phases. The target data must also be at least 1.7 A. Acorn is unlikely to help at lower resolutions, but this resolution limit can be changed with the ACORnres keyword.
MrBUMP prints out the correlation coefficient for medium E values from Acorn. An increase
in these correlation coefficients over Acorn cycles is a good sign that you have the correct
solution (the absolute value of the CC may be low, because these are not the strongest E values).
The columns ECOUT, PHIOUT and WTOUT from Acorn can be used to generate high quality maps to
help model re-building.
[Default False]
Resolution limit for applying the Acorn phase improvement procedure.
[Default 1.7]
Perform automated model building using Buccaneer.
[Default True]
Number of autobuild-refine cycles to carry out in Buccaneer.
[Default 5]
Perform automated model building using ARP/wARP.
[Default False]
Number of autobuild-refine cycles to carry out in ARP/wARP.
[Default 5]
Perform phase improvement and main-chain tracint using SHELXE.
[Default False]
Number of auto-tracing cycles to perform in SHELXE.
[Default 15]
Perform model building with ARP/wARP and/or Buccaneer after SHELXE.
[Default False]
Perform model building with ARP/wARP after SHELXE (SXREBUILD must be set to True).
[Default False]
Perform model building with Buccaneer after SHELXE (SXREBUILD must be set to True).
[Default True]
Use the phases generated by SHELXE (.phs file) in the subsequent rebuild in ARP/wARP
and or Buccaneer (SXREBUILD must be set to True). If USEPHS is set to false model building will
use the c-alpha trace generated by SHELXE as a starting point.
[Default True]
If true, program will do molecular replacement for all search models in the enantiomorphic spacegroup, as
well as in the HKLIN spacegroup, if an enantiomorph exists for the target data spacegroup. MrBUMP will
identify the better spacegroup for each model. For good MR solutions, the correct spacegroup should
be identified. For wrong or marginal solutions, it may be harder to distinguish the correct spacegroup.
[Default False]
Use this keyword to specify a directory where MrBUMP can search for the PDB files it needs for
generating search models. This can help reduce the number of downloads from the PDB databases on
the internet. Mainly useful for users with slow connections and cases where a user wishes to run
several jobs requiring similar search models. PDB files should take the form <PDB ID>.pdb
(e.g. 1nio.pdb). Also, the full path to the directory should be specified.
[Default Not set]
If you have a local mirror of the PDB available through the file system, you can instruct MrBUMP
to access it for the PDB files that it needs using this keyword. Give it the full path to the
location on this of the top level directory for the PDB database. Note that the PDB mirror must have
the standard file hierarchy for the PDB database. The files should be stored in directories named
according to the middle two characters in the PDB ID code. The files should also be gzipped and
stored in the format pdb<PDB ID>.ent.gz. For example, the file for PDB code 1nio
should be <path to PDB directory>/ni/pdb1nio.ent.gz.
[Default Not set]
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]
For use in combination with the CLUSTER keyword. This is the type of batch system that jobs will be submitted to.
Currently, the Sun Grid Engine (SGE) and Portable Batch System (PBS) systems are supported.
[Default SGE]
This is the maximum number of jobs allowed to be submitted to a cluster system at any one time. Set this value if you
want to prevent MrBUMP from overloading an open cluster system.
[Default Unlimited]
Cluster submission command. Arguments to the cluster submission command can also be provided through this keyword. e.g.
QSUB qsub -l vmem=500MB,walltime=02:00:00.
[Default qsub]
If true, the program will remove the files generated for models that were marked as "Failed" solutions. Also,
any files in the scratch area will be removed. This is to cut down on disk space usage.
[Default False]
If true, the program will delete surplus files as it progresses. These include both Molrep and Phaser output files, scratch
files, log files, downloaded PDB files and sequence alignment files. This reduces considerably the disk footprint of a MrBUMP
job. For Phaser and Molrep (on unix systems) a shell script is created to allow for the re-running of the jobs should further
investigation be needed.
[Default False]
Use the python 'pickle' function to output the main data structures into a pickle file. Mainly useful for two-step
runs of MrBUMP - 1. Model search, 2. Molecular Replacement using the previous model generation directory.
[Default True]
This keyword, if set to True, enables an internet connectivity check at the outset of a job. The test involves
connecting to each of the PDB file servers specified and attempting to download a PDB file. If all of the download
attempts fail, the process will report an error and exit the program. This is a possible indication of a network
connection problem or the need for the user to set a proxy server. It can be disabled in situations where PDB files
are sourced from a local folder and a network connection is not required. When set to True, this option also
invokes a PDB file server connecting time script. This script tests how long it takes to retrieve a PDB file from
each of the commonly used PDB file servers (UK, USA and JAPAN). The quickest one is then used to retrieve files
at later stages in the program.
[Default True]
If true MrBUMP will give a more verbose output. Also, temporary directories will not be
deleted at the end of the job. For Phaser/Molrep and Refmac jobs, shell scripts to re-run these jobs on their own
will be created in the mr or refine directories for the particular search model (not on Windows).
[Default False]
If you need to use a proxy server to access the internet you should set it using PROXYSERVER. MrBUMP
uses several on-line services and databases (e.g. the PDB) and thus requires internet access. It is possible to
run MrBUMP without internet access by turning off the FASTA, SSM and PQS searches and using locally stored PDB files
as input search models. The proxy server is set in the environment in which MrBUMP is running. An example of
a proxy server would be "http://proxy.mysite.com:8080/".
[Default not set]
This keyword allows for the passing in of any Phaser keywords to the underlying call to Phaser. For example "PKEYWORD MACMR
PROTOCOL OFF" will turn the refinement option off for molecular replacement in Phaser. For a list of potential keywords please
see the Phaser wiki documentation page.
[Default not set]
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 MRNUM 10 ENSEMNUM 5 IGNORE 1smw 1smm 1smu MRPROGRAM molrep phaser MAPROGRAM mafft DEBUG True CLUSTER False SCOPSEARCH True SSMSEARCH True PQSSEARCH True MDLM True MDLC True MDLS True MDLP False USEACORN 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 (2007) Acta Cryst. D63, 447-457
In addition, authors of specific programs should be referenced where applicable: