
BMP - version 0.2
Automated search model generation and Molecular Replacememt

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About BMP
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BMP 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 **

BMP 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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BMP 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 BMP go to the bmp-0.2 directory and type:

python setup.py

This will install BMP 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 BMP tasks in CCP4i
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To install the BMP 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 BMP.tar.gz file
      which should be in the folder:
     $CCP4/ccp4i

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

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


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

bmp HKLIN foo_in.mtz SEQIN foo.seq HKLOUT foo_out.mtz XYZOUT foo.pdb 
 
BMP 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 BMP see the bmp.html file in the 
$CCP4/html folder.


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Authors
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Ronan Keegan, CCP4, Daresbury Laboratory
Martyn Winn, CCP4, Daresbury Laboratory
