MAPMASK (CCP4: Supported Program)

NAME

mapmask - map/mask extend program

SYNOPSIS

mapmask MAPIN/MSKIN/MAPIN1/MSKIN1 foo.map [ MAPIN2/MSKIN2 bar.map ] [ XYZIN foo.pdb ] [ MAPOUT foobar.map ] [ MSKOUT foobar.msk ]
[Keyworded Input]

DESCRIPTION

`mapmask' is a general map and mask manipulation program. It will change the extent of a map or mask file, re-order a map or mask, scale a map or mask, and generate a mask from a map and vice versa. It will also produce a print out of arbitrary map or mask sections. It can combine two input maps or masks to produce a sum or product map, or a solvent flattened/flipped map.

It can be used in conjunction with SFALL to make a solvent mask, which can be used for solvent flattening using 'dm' or FLATMAP. In this case SFALL is used to make a atom map, and then MAPMASK is used to mask the non-zero areas of this map.

Scaling options from Andrew Leslie's FLATMAP program can be used to scale the map for solvent flattening (SCALE card). Jan Pieter Abraham's solvent flipping and density truncation techniques may be applied (SOLV card).

INPUT/OUTPUT FILES

MAPIN/MAPIN1/MSKIN/MSKIN1

Input map or mask. If MAPIN or MAPIN1 is specified, the values of the map grid points will converted to real numbers (even if the input file is a mask). If MSKIN or MSKIN1 is specified, the values of the grid points will be set to 0 or 1 (even if the input file is a real map).

MAPIN2/MSKIN2

Second input map, used when combining maps or performing solvent flattening (used by SOLV, MAPS cards). Must be on the same grid as the first input map.

MAPLIM

is for use with XYZLIM MATCH option.

XYZIN

is for use with BORDER option.

MAPOUT

is an output map.

MSKOUT

is an output mask, 1 wherever MAP>MSKCUT and 0 elsewhere.

Either MAPOUT, or MSKOUT, or neither, or both may be assigned. If both are assigned then MAPOUT will contain the real map values and MSKOUT the values 0/1.

KEYWORDED INPUT

Possible keywords are:

AXIS, BORDER, EXTEND, MAPS, MASK, MODY, PAD, PRINT, SCALE, SOLV, SYMMETRY, XYZLIM.

XYZLIM [ASU] [CELL] [MATCH] <x1> <x2> <y1> <y2> <z1> <z2>

Set the output map extent as `extend'. <x1>-<z2> are given in grid units or in fractional coordinates. It is possible to automatically extend to the CCP4 default asymmetric unit, or a whole unit cell, by specifying `XYZLIM ASU' or `XYZLIM CELL'. It is also possible to extend the map to match another map (given as MAPLIM) by specifiying `XYZLIM MATCH'. The default is to keep the extent of the input map.

BORDER <n>

Extend the map to cover the volume of a coordinate model given in XYZIN, as `extend'. <n> is the border in Angstrom around the edge of the model.

EXTEND COPY | XTAL | OVERLAP

Selects how the map is to be extended.

COPY: copies density from the input to the output map without applying symmetry or cell repeat.
XTAL: applies both symmetry and cell repeat to generate density outside the input map extent
OVERLAP: applies both symmetry and cell repeat to generate density, and when multiple values are available for a grid point, the highest is taken. This option can be used to generate a solvent mask from an averaging mask covering the whole complex.

Default: If the input map contains the output map: EXTEND COPY. If the input map must be extended: EXTEND XTAL.

PAD <rho>

Normally if you try to extend a map which does not contain at least an (arbitrary) asymmetric unit, mapmask will give an error since it will be impossible to generate some of the map. PAD <rho> supresses the error message and specifies a density value <rho> to be used for such regions.

SYMMETRY <spacegroup name or number>

Override the spacegroup of the input map.

AXIS <fast> <medium> <slow>

Change the output axis order. Default is input axis order. <fast>, <medium>, <slow> must be some permutation of X Y Z.

MASK [CUT <mskcut>] [FRAC <mskfrc>] [VOLUME <mskvol>]

Set the threshold value for making a mask from a map: all density values above this level in the final map will be set to 1.0 in the output mask if one is specified.

CUT <mskcut>: sets the density cutoff value directly.
FRAC <mskfrc>: sets the fraction of the output mask that should be above the threshold. This is used when making a solvent mask, and will work correctly on a unit cell or asymmetric unit.
VOLUME <mskvol>: sets the volume of the mask that should be above the threshold as a fraction of the unit cell volume. This is used when making an averaging mask from a correlation map (see MAPROT).

MODE <logical_name1> [ <logical_name2> ]

[Optional]
Overrides the default mapmask behaviour of looking for any assignment or file with a likely name. The names correspond to logical assignments on the command line (e.g. MODE MSKIN MAPIN2). This keyword is not compulsory but is recommended to explicitly ensure that the correct data is being used as input.

PRINT MAP <axis> [ <first> [ <last> [ <step> ]]]

Print out map sections using the specified section axis. <axis> must be one of X/Y/Z and specifies the section axis. <first>, <last> and <step> specify the range of sections to print. The density values are output as integers, and so this command will normally be used in conjunction with the SCALE card.

PRINT MASK <axis> [ <first> [ <last> [ <step> ]]]

Print out mask sections using the specified section axis. <axis> must be one of X/Y/Z and specifies the section axis. <first>, <last> and <step> specify the range of sections to print. Density values below the current density cutoff will be marked as `*', density values above the cutoff as ` '.

SCALE [FACTOR [c1 [c2]]]

Multiply the map by <c1> and add <c2>. Thus rho'=rho*<c1>+<c2>. Default <c1>=1.0, <c2>=0.0.

SCALE [SIGMA [c1 [c2]]]

Scale the map to have a standard deviation of <c1> and a mean of <c2>. Default <c1>=1.0, <c2>=0.0.

SCALE [MEAN [rhop [rhos]]]

Scale the map so that the mean of the protein region is <rhop> and the mean of the solvent region is <rhos>. This option attempts to put the density on an absolute scale and depends on the low resolution terms being used in the map calculation. MSKIN2 must be assigned. Default <c1>=0.433, <c2>=0.330.

SCALE [RATIO [ratio]]

Scale the map so that the standard deviation of the protein region is <ratio> times the mean of the protein region. As the values of the electron density are approximately normally distributed about the mean, one can use standard tables of the area under a Gaussian curve. Thus <ratio>=0.5 corresponds to approximately 31% of the grid points in the protein being negative, <ratio>=1.0 corresponds to 16% being negative. Default <ratio>=1.0.

SOLV [FLIP <flipfac>] [ATTN <attnu>]

Perform solvent flattening on MAPIN1 using the mask MSKIN2. If FLIP is specified, the density shifts are multiplied by <flipfac>, thus <flipfac>=1.0 corresponds to solvent flattening, <flipfac>=2.0 corresponds to solvent flipping. If ATTN is specified, then negative density in the protein region is multiplied by <attnu>. <attnu>=0.0 corresponds to density truncation. Default <flipfac>=1.0, <attnu>=1.0.

MAPS ADD/MULT

Combine maps by addition or multiplication. No scaling is performed. MAP/MSKIN1 and MAP/MSKIN2 must be specified.

EXAMPLES

Simple unix example script found in $CEXAM/unix/runnable/

mapmask.exam (Contains several examples of how mapmask can be used).

(A vms version found in $CEXAM/vms/mapmask.com)

....and non runnable examples in $CEXAM/unix/non-runnable/

mapcutting (using ncsmask, mapmask and overlapmap).