NCSMASK (CCP4: Supported Program)
- averaging mask manipulation program
This program performs operations on non-crystallographic symmetry
masks. It is ideal as a precursor to `dm', since it contains a
more sophisticated treatment of mask overlap, and may avoid some
problems commonly caused by poorly defined masks.
Input can be from a PDB file, in which case a mask is generated from
spheres around all atoms. A crude 'sphere mask' can be constructed by
making a PDB file with only a few atoms and specifying a large radius.
Alternatively input can be from a CCP4 format map/mask file.
The mask may then be modified by expanding or contracting, smoothing
the boundary, reducing from a multimer to a monomer (in some cases),
removing crystallographic- or non-crystallographic symmetry overlap
and altering the mask box size.
This program should not normally be used for generating solvent masks, since
it does not impose crystallographic symmetry or unit cell repeat. See
for further details. However, these masks can be used in DM 1.7.1 or later.
The GRID and SYMMETRY cards are useful if input is from a .pdb file,
otherwise the information is taken from the input mask header. Available keywords are:
is the input PDB file
is the input mask file
is the output mask file
Set the sampling grid over the unit cell to <nx>*<ny>*<nz>.
The default is 1.0 Angstrom spacing.
Alternatively, the SPACING subkeyword allows you to set the grid spacing; if
only x is specified then this gives x Angstrom spacing along all
axes, otherwise x, y and z are the spacings along each
The GRID keyword is ignored if a mask is input.
Set the spacegroup symmetry for the mask. The default is taken
from the input mask if a mask is input, or P1 if a .pdb file is input.
Change the default output axis order. The first axis specified will
Changes the default mask extent. <x1>-<z2> are either in grid
units or fractional coordinates. If the new extent is smaller
than the input mask extent, the input will be truncated, if
the new extent is larger the mask will be padded with zeros.
The default is either the extent of the input mask or the
extent of the input .pdb file + sphere radius + 3.0 Angstrom.
See however the NOTRIM card.
Set the sphere radius for building a mask out of atoms. Default=3.0
Angstrom. A much larger value could be used to build a mask around
C-alpha or sulphur coordinates, for example.
Pick the <num> largest connected regions of the mask, and delete
all others. `PEAK 1' is particularly useful for tidying up a
correlation mask (see maprot).
Expand/contract the mask. This function expands the mask by <rad>
Angstrom in all directions. The mask will not be expanded beyond the
current mask extent, if this is required the XYZLIM card should be
used to increase the mask extent. A negative value will contract the
Smooth the mask using a sphere of radius <rad>. This will eliminate
features smaller than <rad> from the surface of the mask. Maximum
radius ~5 grid points.
Enter NC-symmetry elements for overlap removal. (Note that this card
has the same format as the `dm' `AVERAGE' card). This card is followed by
<nncs> rotation/translation matrices on subsequent lines in either
CCP4 or O/RAVE format.
- CCP4 Formats (see also lsqkab):
ROTATE EULER <alpha> <beta> <gamma> (Euler angles)
TRANSLATE <t1> <t2> <t3>
ROTATE POLAR <omega> <phi> <kappa> (Polar angles)
TRANSLATE <t1> <t2> <t3>
ROTATE MATRIX <r11> <r12> <r13> <r21> <r22> <r23> <r31> <r32> <r33>
TRANSLATE <t1> <t2> <t3>
- O/RAVE Format
<r11> <r21> <r31>
<r12> <r22> <r32>
<r13> <r23> <r33>
<t1> <t2> <t3>
x' = <r11>x + <r12>y + <r13>z + <t1>
y' = <r21>x + <r22>y + <r23>z + <t2>
z' = <r31>x + <r32>y + <r33>z + <t3>
(note that the rotation matrix is transposed with respect to CCP4
These are the operations which map the density in the region covered
by the input mask onto the other equivalent regions. The first
operator must be the identity matrix. The mask is input in CCP4 mask
format on the input file label MSKIN, and should cover
just one monomer or averaging domain, NOT the whole unit cell.
Reduce a multimer mask to cover only a monomer. This option will
generate a mask covering an arbitrarily chosen monomer from a multimer
in the case where the NCS consists ONLY of a SINGLE PROPER ROTATION
AXIS of any order. An arbitrary segment covering an angle of
2*pi/<nncs> is selected and the rest of the mask is removed.
Perform overlap removal. Overlap removal will be performed by
removing pixels from the surface of the mask. The mask is overlapped
with its crystallographic- and non-crystallographic symmetry related
partners (see SYMMETRY and AVER cards). The overlap removal calculation
may not remove all overlap on the first cycle, if <ncycle> is
specified, overlap removal will be repeated this number of times.
Disable mask trimming. The default is to reduce the mask extent to
obtain the minimum box which will contain the final output mask. With
NOTRIM, the mask extent will be the same as the input mask or the
values on the XYZLIM card if it is present.
The calculations are performed in the following order:
If you want to do them in a different order, run the program several
Read your output. When removing overlap, check that the input and
output masks fill a sensible volume of the unit cell. Don't complain
until you have done this.
To remove the overlap from a mask for input to `dm':
ncsmask mskin ins.msk mskout ins1.msk << eof
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
0.000 0.000 0.000
-0.88284 -0.46960 -0.00849
-0.46899 0.88238 -0.03808
0.02537 -0.02964 -0.99924
82.80000 0.10000 -34.10000
To make a mask from pdb file and remove overlap (note that `dm' doesn't
care about the grid on which input masks are calculated):
ncsmask xyzin ins.pdb mskout ins1.msk << eof
ROTATE EULER 0.0 0.0 0.0
TRANSLATE 0.0 0.0 0.0
ROTATE EULER -29.6 180.0 0.0
TRANSLATE 0.3 0.1 -0.1