label names

• the user chooses the number of labels and the name of each label
• the label (color) name can be up to 30 characters in length
• there can be up to 100 labels (colors)
• each atom or sphere can be left unlabeled, or assigned one color, but not more than one color

label implementation on ligand atoms

• the ligand-atom labels are assigned according to rules given as input to mol2db
• these rules specify the SYBYL atom type (and optionally a second atom type at a user-specified number of bonds away from the labeled atom)

label implementation on receptor atoms

• the receptor sphere labels are added to the sphere cluster file either by the program colsph, or by hand
• colsph evaluates either the Delphi map or the chemgrid force-field map at each sphere center, and the label is determined by which user-specified range this value lies in

matching ligand to receptor labels

• the user explicitly specifies the matching rules in the INDOCK file as pairs of matching colors
• the case_sensitive parameter in the INDOCK file determines whether label names will be case sensitive, (i.e. whether labels such as neutral and NEUTRAL are the same color)
• chemical matching is performed only if it is explicitly requested by the user in the INDOCK file, and if the sphere cluster and ligand database files both contain labels
• if chemical matching is requested, a match is rejected if it includes a ligand-receptor pair in which both atom and sphere are labeled and their labels do not obey the user-specified matching rules

1. Run mol2db on a MOL2 file, giving it the rules to assign labels to atoms.

2. Run sphgen to create a sphere cluster file.

3a. Run colsph on this sphere cluster file to create an output spherecluster file with sphere labels, providing the rules necessary to assign labels to spheres.

or,

3b. Edit the sphere file by hand to add the labels. To do this, list the allowed colors, one per line, beneath the header line in the sphere cluster file. Next, change the last column of each sphere to an integer corresponding to the desired color. For example, 1 corresponds to the first color listed, 2 corresponds to the second, and so on. 0 corresponds to no color, and is considered unlabeled.

4. Run DOCK 3.5 with a keyword-format INDOCK file with the keyword chemical_matching specified and the match rules explicitly stated.

Tell me more about how to use chemical matching!