2.22 ********************
* MAPORTH WRITE-UP *
********************
This program orthogonalizes an electron density map for later use
with programs LSQROT or LSQROTGEN. This program is only needed if one
wants to refine the noncrystallographic symmetry operator(s), and even
then only if the unit cell is not orthogonal. One generally extracts a
region from the map encompassing one dimer, trimer etc. with MAPVIEW
or EXTRMAP, and inputs only the extracted map here for
orthogonalization. One can optionally othogonalize an input mask file
in addition to the map if desired, as may be the case if the mask will
be used to delineate volumes to use in the refinement.
INPUT DATA (UNIT 5)
CARD I PAMFIL (free format)
PAMFIL = Input file specifying cell parameters, symmetry,
used only to get "running log" file.
CARD II INPMAP (free format)
INPMAP = Input (non-orthogonal) map, from EXTRMAP or
MAPVIEW
CARD III IRANGE (free format)
IRANGE = 0 for normal operation.
= 1 to simply compute orthogonal coordinates for
all points in input map, and ouput range (in
orthogonal coordinates) which just encompasses
all of the input map. The range can then be used
to determine map parameters for a subsequent run
with IRANGE=0.
******** following CARDS read only if IRANGE = 0 ********
CARD IV OUTMAP (free format)
OUTMAP = Output map file to contain orthogonal map.
CARD V a', b', c' (free format)
a' = Cell lengths (in angstroms) for the output orthogonal
map. They should be large enough to cover the same
b' = volume as the input map, when it is referenced in the
orthogonal system. New orthogonal cell a',b',c' has a'
c' = along old a, b' along old c* cross old a, c' along a'
cross b' ( i.e. old c*)
CARD VI MGX,MGY,MGZ,LXMN,LXMX,LYMN,LYMX,LZMN,LZMX (free format)
MGX =
Number of grid points defining one "cell length" along
MGY = the respective orthogonal axis. Implicitly defines grid
spacing as del x = a'/MGX, del y = b'/MGY and del z = c'/MGZ
MGZ =
LXMN, LXMX =
Minimum, maximum grid index defining output map region
LYMN, LYMX = such that x (fractional) = LX * (del x) / a' etc.
There are no restrictions on magnitudes or signs.
LZMN, LZMX =
CARD VII IMASK (free format)
IMASK = 0 For no mask input.
= 1 for input mask corresponding to input map. The mask will
also be "orthogonalized" so that it can be used by LSQROT
or LSQROTGEN.
******** following cards read ONLY if MASK=1 ********
CARD VIII INPMSK (free format)
INPMSK = Input mask file, from MAPVIEW or EXTRMSK
CARD IX OUTMSK (free format)
OUTMSK = Output (orthogonal) mask file
NOTES: If a mask is input, it must coincide exactly with the input
map.
******** FILES ********
INPUT MAP FILE (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
INPUT MASK FILE (BINARY)
Header record identical to map file.
Mask records similar to normal map records except that
the mask values are written as FORTRAN type "BYTE" (INTEGER*1).
Only grid points with mask values of 0, 10, 20, 30, 40 etc will
be transformed (i.e. inside envelope masks 1,2,3,4,5 etc,
respectively).
OUTPUT MAP FILE (BINARY)
Identical (in structure) to input map file, but cell, map and
density values correspond to the orthogonal "cell".
OUTPUT MASK FILE (BINARY)
Header record identical to map file.
Mask records similar to normal MASK records, but cell, map and
mask values correspond to the orthogonal "cell".