MAPMASK (CCP4: Supported Program)
- map/mask extend program
`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 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).
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.
is for use with XYZLIM MATCH option.
is for use with BORDER option.
is an output map.
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.
Possible keywords are:
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
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
EXTEND COPY | XTAL | OVERLAP
Selects how the map is to be extended.
Default: If the input map contains the output map: EXTEND COPY.
If the input map must be extended: EXTEND XTAL.
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
copies density from the input to the output map without applying
symmetry or cell repeat.
applies both symmetry and cell repeat to generate density outside
the input map extent
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.
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> ]
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
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.
Combine maps by addition or multiplication. No scaling is
performed. MAP/MSKIN1 and MAP/MSKIN2 must be specified.
Simple unix example script found in $CEXAM/unix/runnable/
(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/
(using ncsmask, mapmask and overlapmap).