OVERLAPMAP (CCP4: Supported Program)

NAME

overlapmap - calculates the average of two maps

SYNOPSIS

overlapmap mapin1 foo.map mapin2 bar.map [ mapin3 baz.map ] mapout quux.map
[Keyworded input]

DESCRIPTION

overlapmap 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:
  1. Average MAPIN1 and MAPIN2 with output to MAPOUT (MAP AVERAGE).
  2. Sum the density from MAPIN1 and MAPIN2, output to MAPOUT (MAP ADD).
  3. Set density to zero in MAPOUT if present in MAPIN1 (i.e. non zero MAPIN1 density). Otherwise grid points in MAPOUT are set to MAPIN2 (MAP EXCLUDE). This requires MAPIN1 has some grid points which are EXACTLY zero; you are unlikely to have this unless you have generated a map from coordinates.
  4. Set density in MAPOUT to MAPIN2 if the grid point in MAPIN1 > 0. Otherwise set to zero (MAP INCLUDE).
  5. Correlate the density between MAPIN1 and MAPIN2 over a given volume, which may be either the whole map, the volume occupied by a given residue or atom, or section by section (there is no MAPOUT in this mode). There are three correlation modes (CORRELATE ...), two of which require a third map array (see MAPIN3). This is used to flag which grid points are associated with each residue or atom and are therefore to be included in their correlation coefficient calculation.

    Remember the correlation transcends any need to scale the 2 maps. Below is the definition of the correlation coefficient: 

    
corr. coeff.  =    (<x y> - <x><y>) / 
              ( sqrt(<x^2> - <x>^2)  *  sqrt(<y^2> - <y>^2) )
    where x represents the density values from one map and y the values from the other.
    < > represents the mean value of the quantities inside the bracket.
  6. Calculates a Real Space R factor à la Branden/Jones (reference [1]). 
    
Real space R factor =
          Sum(RHO_obs - RHO_calc)/Sum(RHO_obs + RHO_calc)
    summed over all points within a residue. This requires that RHO_obs and RHO_calc are ON THE SAME SCALE. It is also sensitive to the atom radius you chose in SFALL. Eleanor Dodson believes it is not as useful as the correlation coefficient. MAPIN3 will be needed for this mode of operation calculated from SFALL in the RESMOD mode - see below.

KEYWORDED INPUT

The available keywords are:

CHAIN, CORRELATE, MAP, PATTERSON, REAL SPACE R

MAP [ ADD | AVERAGE | EXCLUDE | INCLUDE ]

ADD <scale1> <scale2>
add <scale1>*map1 + <scale2>*map2 and output new map. (Default <scale1> = <scale2> =1.)
AVERAGE
average two maps and output new map.
EXCLUDE
exclude points from output map if they exist in MAP1. Any grid point that is is not zero in MAP1 will be set to zero in MAPOUT. Grid points in MAPOUT will be set to the value in MAP2 if the grid point in MAP1 is zero.
INCLUDE
include points in output map from MAP2 if they exist in MAP1. The value of the grid point in MAPOUT will be that of MAP2 if the grid point in MAP1 > 0. Otherwise the point in MAPOUT will be set to zero.

CORRELATE [ SECTION | RESIDUE | ATOM ]

SECTION
correlation is section by section.
RESIDUE
correlation is residue by residue.
ATOM
correlation is atom by atom.

REAL SPACE R

tabulated 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 ([2]). <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.

NOTES

MAPIN3 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).

SEE ALSO

fft(CCP4),
sfall(CCP4),
maprot(CCP4)

REFERENCES

  1. Branden C. and Jones A., Nature 343 687-689 (1990)
  2. Jones Y. and Stuart D, Proc. of CCP4 Study Weekend on Isomorphous Replacement And Anomalous Scattering, 1991 39-48.

EXAMPLES

Correlation by residue

  • overlapmap.exam

    • 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.