2.26 *******************
* BLDCEL WRITE-UP *
*******************
BLDCEL is a program to rebuild an electron density (and optionally
a mask) map covering one complete unit cell, from an input map (and
mask) covering an asymmetric unit. Typically an asymmetric unit
encompassing a dimer, trimer etc is extracted from a FSFOUR map by
EXTRMAP or MAPVIEW, and averaging is done only within that submap in
program MAPAVG. The averaged asymmetric unit map and corresponding
mask is input here, along with the FSFOUR map from which the
asymmetric unit map was extracted. An exact copy of the FSFOUR map is
first created, but then density values at grid points which lie within
the averaging envelopes are replaced by their values from the averaged
map. Averaged density also replaces values at grid points related by
crystal symmetry to the input averaged map. Thus the output map
corresponds to the averaged map, except that it covers one full cell
and conforms to the space group symmetry. Density at values which were
not averaged simply retain their values from the original map. The
format is identical to that produced by FSFOUR, thus this map is
suitable for inversion, peak search etc. If desired, the input
asymmetric unit mask can also be expanded to a full cell mask. There
is never any need to do this for averaging purposes, but it is useful
if one wants to use SOLVENT FLATTENING masks which were edited by
program MAPVIEW. In that case one would extract a region from the
solvent mask (created by BNDRY, option 1) which covers an asymmetric
unit, by using MAPVIEW or EXTRMSK. Edit the extracted solvent mask in
MAPVIEW. Then use the MAKE ASU expansion option in MAPVIEW to create
an edited mask file obeying crystal symmetry. Finally, input the
edited mask file here, and request that it also gets expanded to a
full cell. The output mask file then can be used for solvent
flattening, since it covers a full cell, obeys space group symmetry
and has the same structure as a normal solvent flattening mask.
INPUT DATA (UNIT 5)
RECORD 1 PAMFIL (free format)
PAMFIL = Input parameter file specifying cell and symmetry
information.
RECORD 2 INPMAP (free format)
INPMAP = Input map file (unaveraged, full cell, from
FSFOUR)
RECORD 3 OUTMAP (free format)
OUTMAP = Output map file (full cell, averaged)
RECORD 4 INPASU (free format)
INPASU = Input map (averaged, asymmetric unit)
RECORD 5 INPMSK (free format)
INPMSK = Input mask (asymmetric unit)
RECORD 6 NEWMSK (free format)
NEWMSK = 0 for no expansion of mask to full cell
= 1 to also expand input mask to full cell
RECORD 7 OUTMSK (free format)
******* include this record only if NEWMSK=1 *******
OUTMSK = Output mask file (full cell)
***** FILES *****
INPUT MAP FILE "INPMAP" (BINARY)
Standard FSFOUR map, default orientation i.e. NORN=0
OUTPUT MAP FILE "OUTMAP" (BINARY)
Same structure as input file "INPMAP"
INPUT MAP FILE "INPASU" (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 "INPMSK" (BINARY)
Header record identical to map file INPASU.
Mask records similar to normal map records in INPASU 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 used (i.e.
inside envelope masks 1,2,3,4,5 etc, respectively).
OUTPUT MASK FILE OUTMSK (BINARY)
Same structure as input mask file INPMSK, but covers full cell