
MrBUMP - version 0.2.5
Automated search model generation and Molecular Replacememt

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New in version 0.2.5
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1. Ability to include specific "chains" in the search models.
2. User entry of no. of molecules in the a.s.u.
3. User entry for PACK keyword in Phaser (clashing tolerence).

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About MrBUMP
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MrBUMP is an automated scheme for Molecular Replacement. Given 
a target sequence and experimental structure factors, it will 
search for homologous structures, create a set of suitable 
search models from the template structures, do molecular 
replacement, and test the solutions with some rounds of restrained 
refinement.

* IMPORTANT * IMPORTANT * IMPORTANT **

MrBUMP relies heavily on the use of web-based sevices and applications 
for carrying out the template search part of the procedure. It also
retrieves PDB files from the web to construct the search models. If
you are sensitive about your target sequence data it is suggested that
you download and install the fasta34 program so that you can run the 
sequence-based searches locally. This is availble from the EBI site:

ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/

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Installation
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MrBUMP has a few dependencies which must be present on your system 
before it can be installed.

    * Mandatory:
          o CCP4 6.0 or higher,
          o Python 2.3 or later,
          o Mafft or Clustalw,
          o Gnuplot.
    * Optional:
          o Fasta34,
          o Perl + SOAP-Lite perl module (for SSM search).

To install MrBUMP go to the mrbump-0.2 directory and type:

python setup.py

This will install MrBUMP under your CCP4 installation or in the 
current directory if the user does not have permission to 
write to the CCP4 folder.

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Installing the MrBUMP tasks in CCP4i
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To install the MrBUMP CCP4i task carry out the following steps:

  1. Start the CCP4i gui, click on the 'System Administration'
     tab and select 'Install/uninstall Tasks'.
 
  2. Where it says 'Run the Installation Manager to' select 
     'install a new task'.

  3. Under the 'Install Package Information' section, where
     it says 'Task Archive', browse to the MrBUMP.tar.gz file
      which should be in the folder:
     $CCP4/ccp4i

  4. When you have selected the MrBUMP.tar.gz file click on the
     'Apply' button.

  5. Restart ccp4i. The MrBUMP tasks should appear in the 
     'Program List' and 'Molecular Replacement' menus.


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Running MrBUMP
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MrBUMP can be used via the CCP4i gui or from the command line. Here
is an example of how to use MrBUMP on the command-line:

mrbump HKLIN foo_in.mtz SEQIN foo.seq HKLOUT foo_out.mtz XYZOUT foo.pdb 
 
MrBUMP is similar to other CCP4 programs in that it requires keywords.
The user will be prompted for these keywords at the begining of a 
job or they can be written to a file and passed into the program 
on the command line.

For details of the keywords for MrBUMP see the mrbump.html file in the 
$CCP4/html folder.


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Authors
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Ronan Keegan, CCP4, Daresbury Laboratory
email: r.m.keegan@dl.ac.uk

Martyn Winn, CCP4, Daresbury Laboratory
email: m.d.winn@dl.ac.uk
