
Edit the parameter file, 
<font color=blue><B>ligplus.par</B></font>, which you wil find in the
<font color=blue><B>lib/params</B></font> subdirectory of the
directory containing the
<font color=blue><B>ligplus.jar</B></font> file.

The parameters you will need to edit to customize
<B>LIGPLOT<SUP>+</SUP></B> for your system are the following:

<H3>PDB directories and ftp address</H3>

PDB files are most conveniently identified simply by the 4-character
PDB code or identifier. If your system contains one or more locations
where PDB files are stored, you can define a "template" path which
will allow <B>LIGPLOT<SUP>+</SUP></B> to find the relevant PDB file
from its 4-character code alone.

<P>
Alternatively, if you are connected to the internet when you run
<B>LIGPLOT<SUP>+</SUP></B>, the required file can be retrieved by ftp
from a given ftp site.

<P>
The parameters describing the location of PDB files are named:

<font color=red><B>PDB_DIR</B></font>,
<font color=red><B>PDB_DIR1</B></font>,
<font color=red><B>PDB_DIR2</B></font>, etc, and should be entered in
the order they are to be searched by the program. Any number of
directories can be defined here.

<P>
In each case, the template describing the location of the file
represents the 4 characters of the PDB code as <font
color=green><B>abcd</B></font>. These appear in the template within
square brackets.

<P>
For example, the template

<P>
<font color=green><B>C:/roman/pdbsum/pdb/pdb[abcd].ent</B></font>

<P>



<P>
<B>Local PDB files</B>


<H3>The Het Group dictionary</H3>

<B>LIGPLOT<SUP>+</SUP></B> gets its information about ligand molecules
from the Het Group Dictionary. This defines the atom names,
connectivities and bond orders of every Het Group in the PDB. An old
(June 2009) version of this dictionary is supplied with the
program. However, you might with to keep this file updated by
periodically downloading from the wwPDB at:

????????????

Simply overwrite the file in the 

<P>
Alternatively, change the path of
<font color=red><B>HET_GROUP_DICTIONARY</B></font> from
<font color=green><B>lib/data/components.cif</B></font> to the
absolute path on your system where a regularly-updated version of this
file resiudes.


