2.25 *****************
* SKEW WRITE-UP *
*****************
Program SKEW, for the conversion of a "normal" input map (and
optionally, mask) to a "skewed" cell, such that the new b axis will
correspond to a specified direction. The input map is usually created
by MAPVIEW or EXTRMAP, and the input mask (if any) is usually created
by MAPVIEW or EXTRMSK. This program is generally used if the input
noncrystallographic symmetry operator is purely rotational, with the
rotational order given by 360/N where N is an integer, i.e. pure
twofolds, threefolds etc. In that case it is much easier to create the
averaging mask (in MAPVIEW) when looking directly down the
noncrystallographic symmetry axis, and convert it back to the standard
orientation (via program TRNMSK) for use in averaging cycles. Thus one
would use MAPVIEW or EXTRMAP to extract a region from the map
encompassing the dimer, trimer etc. to be averaged, skew that
extracted map, input it into MAPVIEW to trace out the mask in the
skewed direction, and then convert the skewed mask from MAPVIEW back
into the standard orientation with TRNMSK. One would then input the
standard (non-skewed) mask into MAPVIEW again, along with the submap
from which the skewed map was originally created, and invoke the
MAKE ASU option. This last step allows one to check for redundant
entries (by CRYSTAL symmetry) within the envelope, and to correct them
prior to saving the final mask for averaging.
INPUT DATA (UNIT 5)
CARD I PAMFIL (free format)
PAMFIL = Input parameter file containing cell and symmetry
information, used only to get "running log" file
CARD II INPMAP (free format)
INPMAP = Input map file, from MAPVIEW or EXTRMAP
CARD III PHI, PSI, OX, OY, OZ (free format)
Spherical polar angles defining direction of
PHI = noncrystallographic symmetry axis, oriented with respect
to orthogonal frame X,Y,Z with X along a, Y along c* cross
PSI = a, and Z along X cross Y (i.e. c*). PSI = angle between NC
symmetry axis and +Y axis. PHI = angle between projection
of NC symmetry axis on XZ plane and +X axis. +PHI= CCW
rotation about +Y axis as measured from +X axis.
OX =
Origin of NC symmetry rotation axis, in angstroms with
OY =
respect to the orthogonal axes. The axis passes through
this point.
OZ =
CARD IV IRANGE, IMASK (free format)
IRANGE = 0 for normal operation (coordinate range for OUTPUT
skewed map will be input to the program by the user)
= 1 to determine coordinate range for OUTPUT map which just
encompasses the input volume, output it, and stop.
IMASK = 0 for normal operation (only skewed map created)
= 1 to additionally create skewed mask, from input mask
****** FOLLOWING CARDS READ ONLY IF IRANGE=0 ******
CARD V OUTMAP (free format)
OUTMAP = Output (skewed) map file
CARD VI CELL,MX,MY,MZ, LXMN,LXMX,LYMN,LYMX,LZMN,LZMX (free format)
CELL = length (in Angstroms) for "cell" parameters in "skewed" cell.
MX =
Number of grid points defining one "cell length" along
MY = respective axis in "skewed" cell. Implicitly defines grid
spacing as del x = CELL/MX, del y = CELL/MY and del z = CELL/MZ
MZ =
LXMN, LXMX =
Minimum, maximum grid index defining output map region
LYMN, LYMX = such that x (fractional) = LX * (del x) / CELL etc.
There are no restrictions on magnitudes or signs.
LZMN, LZMX =
****** FOLLOWING CARDS READ ONLY IF IMASK=1 ******
CARD VII INPMSK (free format)
INPMSK = Input mask file (standard orientation)
CARD VIII OUTMSK (free format)
OUTMSK = Output (skewed) mask file.
******** FILES ********
INPUT (AND OUTPUT) MAP FILES (BINARY)
record 1) A,B,C,AL,BE,GA,NX,NY,NZ,IXMN,IYMN,IZMN,IXMX,IYMX,IZMX
with first 6 values REAL*4, next 9 INTEGER*4, lengths in Angstroms,
angles in degrees.
NX =
Number of grid points defining one "cell length" along
NY = respective axis. Implicitly defines grid spacing as
del x = A/NX, del y = B/NY and del z = C/NZ
NZ =
IXMN, IXMX =
Minimum, maximum grid index defining map region such
IYMN, IYMX = that x (fractional) = IX * (del x) / A etc.
There are no restrictions on magnitudes or signs.
IZMN, IZMX =
The map follows as (IYMX-IYMN+1)*(IZMX-IZMN+1) records, with each
containing one row (IXMX-IXMN+1 REAL*4 values) along X, starting at
IXMN. Y is slowest varying, i.e. the file could have been created with
the following FORTRAN code:
DO 30 IY=IYMN,IYMX
DO 20 IZ=IZMN,IZMX
20 WRITE(LU)(RHO(IX,IY,IZ),IX=IXMN,IXMX)
30 CONTINUE
NOTES: If a mask is input, it must coincide exactly with the input
map.
INPUT (AND OUTPUT) MASK FILES (BINARY)
Header record identical to map files.
Mask records similar to normal map records except that the mask values
are written as FORTRAN type "BYTE" (INTEGER*1). Grid points with mask
values of 0, 10, 20, 30, 40 etc correspond to envelope masks
1,2,3,4,5 etc, respectively.