The extend program can be found in the directory $HYD_MAP.
The extend program is a new program based on the existing mbkall program but with the addition of a set of command line arguments. It is designed for the conversion of maps in various formats to map brick format, but it also allows for the extension of maps to a different volume and the generation of compressed O format files for map masks.
The original functionality of mbkall required the following command line arguments:
mbkall ccp4 filein.map fileout.mbk b
1. ccp4 is the original map format.
2. filein.map is the input file name.
3. fileout.mbk is the output file name, i.e., mbk file (the output file type binary/integer/real - binary is the most usual).
The additional functionality uses additional command line arguments (beginning with a "-"), some with parameters. Only the first letter is required for the arguments, since there are no conflicts in the naming convention. If no default is show in square brackets ([ ]), then none is provided.
Extend the map to the limits defined using the -l,-r,-p,-m arguments. No extension of the map occurs unless this argument is provided, and if no limits are defined by other parameters, then the limits are a full cell. If this argument is used, then the -g argument must be specified as well.
Used to define the space group. You should provide a valid space group defined in the symmetry file.
Used to define the full filename for the symops file. The default should be correct if QUANTA has been set up to run.
Defines the limits of extension using a real space box from "xmin" to "xmax", "ymin" to "ymax", and "zmin" to "zmax". Six numbers must be given in the order defined above.
Defines the limits of extension using a real space sphere, from a point and radius. Four numbers must be given.
The limits of extension are defined by the minimum and maximum bounds of all atoms in the given PDB file.
The limits of extension are defined by minimum and maximum bounds of all atoms in the given MSF file.
"Extend" to the same limits as input map
This defines a boundary beyond the limits generated from a PDB/MSF file. It would be normal to use a boundary of 4 Å about a molecule for extension.
Generate an O compressed output file type. This action is independent of the extend functionality and can be used in conjunction with any other argument. This argument should be used where the input file is a map mask and allows the conversion of mask from various formats into the O compressed format which will allow it to be read into QUANTA/X-AUTOFIT/map masks/.
Valid only with the -o option, this defines the cutoff that defines the inside/outside of a mask. Default = 0.5
To extend a map round a set of MSF coordinates.
extend ccp4 mapin.map mapout.mbk b -e -m myfile.msf -b 5 -g r3
To generate a map mask from a CCP4 map file
extend ccp4 mask.map mask.msk b -o
The program when carrying out map extension dynamically allocates memory on run time. The memory required is defined by the volume of the input map and the volume of the output map. If more memory is requested than is available, the program aborts with a memory error.
The program actually runs faster in extend mode (to small volumes - i.e., about a single molecule) than the standard map conversion. This is because in extend mode, the input and output maps are in memory.
There is no requirement about the starting map asymmetric unit and the final position of the extended map; the former and latter need not overlap and need not be in the principle unit cell.