REFMAC (CCP4: Supported Program)

NAME

SYNOPSIS

refmac5 XYZIN foo_cycle_i.brk HKLIN foo.mtz TLSIN tlsin.txt TLSOUT tlsout.txt XYZOUT foo_cycle_j.brk HKLOUT foo_cycle_j.mtz
[Keyworded input]

DESCRIPTION

REFMAC now has two 'modes': REVIEW which only checks and updates the input model to establish that the geometric restraints can be properly set up, and the standard REFINE mode documented in keywords.

REFMAC in REVIEW mode

1. Checking the model coordinates and writing an extended output set of coordinates.

   This replaces and extends one of the roles of PROTIN. The input model (or PDB file) will contain coordinates identified by a CHAIN identifier, a RESIDUE (or more precisely, a monomer) identifier (e.g. ALA TYR HEM HOH) and an atom name (e.g. CA or Fe+3). The output file will have the following extra information.

2. Refmac actions: Finding disulphide bonds, and other covalent links.

   REFMAC now does a preliminary distance angles check on the input coordinates and suggests likely di-sulphide bonds and other links. These are written to the output PDB file in the standard PDB format:

   SSBOND   1 CYS A   48    CYS D   48                          1555   2555
   SSBOND   2 CYS B   48    CYS C   48                          1555   2555
   LINK     1   OE1 GLU A 276                CA   CA  W   1     1555   1555
   LINK     1   OE1 GLU A 276                CA   CA  W   1     1555   1555
   LINK     1   OD2 ASP A 307                CA   CA  W   1     1555   2556
   LINK     1   O   HOH W 133                CA   CA  W   1     1555   1555
   

   The LINK record can be modified by the user to include the target distance. In this format: the distance has format F10.5.

   LINK     1   OE1 GLU A 276        2.13400 CA   CA  W   1     1555   1555
   LINK     1   OE1 GLU A 276        2.13400 CA   CA  W   1     1555   1555
   LINK     1   OD2 ASP A 307        2.13400 CA   CA  W   1     1555   2556
   LINK     1   O   HOH W 133        2.40000 CA   CA  W   1     1555   1555
   

3. Refmac actions: Finding cis-peptides.

   REFMAC now does a preliminary survey of cis-peptides and writes the records to the output PDB file.

   CISPEP   1 SER A   26    PRO A   27          0         0.00
   CISPEP   1 HIS A  220    PRO A  221          0         0.00
   

4. Refmac actions: Outputting the sequence and REMARK records.

   REFMAC does not output the SEQRES records to the XYZOUT file. All REMARK records are stripped out; those relevant to refinement are replaced.

   All this output needs to be carefully checked, and edited by the user.

   If this is enough to describe the chemistry of the model completely, the REFINE mode of refmac can be started without any other action. However, if the molecule under study has a novel group REFMAC in REVIEW mode will exit with a message requiring the user to provide a complete chemical description of this.

   Obviously, before starting restrained refinement it is necessary that the chemical properties of each monomer in the model (i.e. the identifier and charge for each atom, the connectivity and bond types with target distances and standard uncertainities, the angles, chiral centres, planar groups, target torsion angles) are described. For the standard peptides, sugars, and nucleotides plus some common ligands these are provided in distributed library files in $CLIBD_MON/. For any other monomers the user must provide their own library.

5. SKETCHER/LIBCHECK actions: These are the tools used within CCP4 for creating a complete chemical description of a novel monomer. The user should first sketch on paper a detailed picture of the expected ligand, showing single and double bonds, hydrogens, chiral centres and planar groups, and possibly atomic charges (for example see Dictionary entry from minimum description). This can be entered into SKETCHER, either by actually adding atoms to the sketch, or by reading in a PDB file with a similar ligand. This can be edited in SKETCHER, and once the user is satisfied that there is a reasonable depiction of the ligand on the screen, SKETCHER will generate a minimal description tabulating all the given information. This minimal description is then extended by LIBCHECK to create a complete monomer description written to the file assigned to LIBOUT.

REFMAC in REFINEMENT mode

The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.

[Program organisation and communication with it is illustrated in the EXAMPLES section.]