Installing pirate:

First you should have a licensed, working install of CCP4 version 5.0
(or 5.0beta). This 'pirate' package contains a time-limited binary of
pirate compiled for Linux/x86, and distributed as proprietary software.

You may install this software for your use within your site for testing
and structure solution. You may not modify or redistribute it.
This software includes Clipper and kiss-fft, see the accompanying
COPYING* files for license details.


There are two ways to install pirate:

 - In your CCP4 distribution (this requires you having access to the
 appropriate account).

 - In your own area (doesn't require any access, but the help buttons
 on the GUI may not work).

If you are reading this, you have presumably already unpacked the main
tar file. This will give you the following files and directories:

 bin/cpirate
 bin/chltofom
 html/cpirate.html
 html/chltofom.html
 reference_structures/makereference.csh
 pirate.tar.gz   (THE GUI)

You will need to take the following steps:
 1. (optionally) copy files into your distribution.
 2. install the new ccp4i GUI components.
 3. make some reference structures.

The steps are as follows:

--

1. COPY FILES INTO YOUR DISTRIBUTION

If you are installing in your CCP4 distribution, setup ccp4 and then
give the following commands:
 cp bin/* $CCP4/bin
 cp html/* $CCP4/html

--

2. INSTALL THE NEW CCP4I GUI COMPONENTS

Start the ccp4i gui. From the 'System Administration' menu (bottom
right) select 'Install tasks'.

If you are installing in your own area, change the installation area
(on the second line down) from 'main CCP4i' to 'Users local CCP4i'.

Now enter the name and path of the file pirate.tar.gz from the
distribution (or use the browse button if you prefer). Hit 'Apply'
to add the new GUI components.

If you are installing in your own area, you must now take an
additional step to tell the GUI where to find the new programs. From
the 'System Administration' menu select 'Configure Interface'. At the
bottom of the 'External Programs' section, click the 'Add a Program'
button twice. Enter the names 'cpirate' and 'chltofom' in the boxes on
the left, and give the full path and filename of the corresponding
programs in the boxes on the right.

--

3. MAKE SOME REFERENCE STRUCTURES

Go to the reference_structures directory. If you are installing in you
main CCP4 directory, you can move this directory into $CCP4 so all
your users can see it.

Now run the makereference.csh script with a list of suitable PDB codes
for which reflection data is available. 
The following list 3 good large structures (1dll, 1ajr, 1bv4), and two
medium structures for extreme solvent cases (1tol 1at6).

 ./makereference.csh 1tol 1dll 1ajr 1bv4 1at6

Protein fractions are as follows: 1tol-33% 1dll-43% 1ajr-50% 1bv4-56% 1at6-64%
Treat results from the two extreme structures wioth suspicion unless the
maps look good.
The old list of small structures was as follows, these can be a bit hit
and miss: 1svn, 1lz8, 1c8u, 1b9m, 1bm3

Note: You will usually receive error messages from 'truncate' while
running these scripts. These are nothing to worry about, and arise from
the fact that a few cif files have I's instead of F's.

Note: if you are behind a firewall, the ftp commands may fail. In
which case you will have to fetch the coordinate and structure factor
files by hand. Put these in the same directory, and edit the script to
comment out the ncftpget commands, then rerun it.
