OVERLAPMAP (CCP4: Supported Program)
NAMEoverlapmap - calculates the average of two maps
SYNOPSISoverlapmap mapin1 foo.map mapin2 bar.map [ mapin3 baz.map ] mapout quux.map
DESCRIPTIONoverlapmap has basically three modes of operation, combining two maps to produce an output map, correlating two maps or generating a real-space R-factor between two maps. Here are the modes in more detail:
The available keywords are:
CHAIN, CORRELATE, MAP, PATTERSON, REAL SPACE R
MAP [ ADD | AVERAGE | EXCLUDE | INCLUDE ]
CORRELATE [ SECTION | RESIDUE | ATOM ]
REAL SPACE Rtabulated residue by residue.
CHAIN <chain_ID> <1st_residue_number> <last_residue_number>Repeat residue numbering by chain, as in SFALL.
PATTERSON <sigmin> sigmax>Calculate a correlation coefficient as in GROPAT (). <sigmin> and <sigmax> are the minimum and maximum grid value/sigma ratio, typically 3. and 10. It is recommended that origin removed difference Pattersons should be calculated.
NOTESMAPIN3 may be assigned to the modified map output of SFALL. This map flags each grid point according to certain criteria; the most useful is the residue flag created by MODE ATMMAP RESMOD. This flags each point in the map space to indicate which atom of a residue it is near (using the Atom Radii specified in SFALL), and whether the atom involved is main chain, or side chain. This is required if you want to use CORRELATE RESIDUE or REALSPACE Rfactor.
The program must have both maps calculated in exactly the same way. Since any Fc map generated from coordinates has a fixed asymmetric unit and AXIS ORDER do them first and make sure your FFT calculation matches that.
EXCLUDE is useful for flattening the protein density when you want to inspect the residual density only. Used in solvent searches and also in the PHASED TRANSLATION function (part of the FFT package). Generate the protein density in SFALL outputting an Fc map.
CORRELATE can be done section by section or by RESIDUE or ATOM. CORRELATE RESIDUE is only possible if MAPIN3 is generated in SFALL outputting an Fc map with mode = mode atmmap resmod).
CORRELATE ATOM is only possible if MAPIN3 is generated in SFALL outputting an Fc map with mode = mode atmmap atmmod).
overlapmap MAPIN1 rnasatomfc.map MAPIN2 rnas2fo_fc.map << END CORRELATE RESIDUES END
Averaging 2 maps
overlapmap MAPIN1 chmi_phase_extend.ext MAPIN2 wang_cycle3.ext MAPOUT chmi_wang_av.map << END MAP AVERAGE END
See also $CEXAM/unix/runnable/mapcorrelation_procedures and $CEXAM/unix/non-runnable/mapcorrelation.exam.