REFMAC (CCP4: Supported Program)

User's manual for the program refmac version 5.0.36

DICTIONARY

How to make a dictionary entry from the coordinate file

Coordinate file formats recognised are PDB, small molecule CIF and mmCIF.

If there is a PDB coordinate file, then REFMAC can be used to create a dictionary entry. In this case the following script should be used:

refmac XYZIN <new_ligand.pdb> XYZOUT <new_ligand1.pdb> \
LIB_IN <my_lib_if_there_is_any.lib< LIB_OUT <my_new_lib.lib>
<< eor
#
#
MODE NEWEntry
MAKE EXIT Yes
#
END
eor

If the ligand contained in the coordinate file is not in the list of the standard entries, the program will create a description for it and add this to the user supplied entry lists specified by LIBIN. An output file will be written to the file specified by LIBOUT (default is new.lib) in the command line. If there is no user supplied entry list (i.e. LIBIN has not been specified) then the created file will contain the new entry only. If desired, this file can be merged with old entry lists using conventional editors (not reccommended).

It is recommended that a new entry description be checked prior to using it in refinement. Especially atom types should be checked. If there are hydrogens, the program usually creates dictionary files correctly. If there are no hydrogens, in many cases the program creates dictionary entries correctly. If coordinates are not good then atom types may not be correct. In this case atom types in the new entry list should be corrected and the program rerun with minimum description.

If the description of a ligand is not as desired by the user, the sketcher can be used to correct the coordinates and the description for it.

After creating new entries and checking them carefully, REFMAC can be run as normal, with new ligand supplied as follows:

refmac ... LIB_IN <my_new_ligands> ... << eor

Command lines to use refmac

eor

Another way of making new entries from coordinates is using LIBCHECK.