2.21 *******************
* MAPAVG WRITE-UP *
*******************
Program MAPAVG, for the averaging of electron density map
regions according to noncrystallographic symmetry. The NC symmetry
related regions may be in the same map, in different maps (crystals)
or both. The program expects the names of all input (unaveraged) map
files, all corresponding mask files, all output (averaged) map files
and the operators defining the noncrystallographic symmetry. The input
map files should be created from FSFOUR maps by running EXTRMAP or
MAPVIEW to extract the map region which encompasses only the dimer,
trimer etc to be averaged for each crystal. For cross-crystal
averaging monomers may be used as well. Each mask map must cover
EXACTLY the same region as its corresponding input map. The mask map
is generally created by MAPVIEW, and possibly transformed by TRNMSK,
although if it is derived from an atomic model it may be created by
MDLMSK. The operators are generally refined by LSQROT or LSQROTGEN
prior to use in averaging. If cross-crystal averaging is done an
additional least squares refinement pass is automatically included
prior to averaging to put the density maps from different crystals
on a common scale. After averaging however, each output map, will be
on the same scale as it was originally input.
INPUT DATA (UNIT 5)
CARD I PAMFIL (free format)
PAMFIL = Name of input parameter file, used only to get the
"running log" filename.
CARD II NCRYST (free format)
NCRYST = Number of different crystals (maps) to be used.
(maximum = 6)
The following block of cards III-VII must be repeated NCRYST times,
once for each crystal.
CARD III INPMAP (free format)
INPMAP = Name of input (unaveraged) map file for this
crystal.
CARD IV INPMSK (free format)
INPMSK = Name of input mask file for this crystal.
CARD V OUTMAP (free format)
OUTMAP = Name of output (averaged) map file for this
crystal.
CARD VI NMOL, (MSK(j), j=1,NMOL) (free format)
NMOL = Total number of molecules related by
noncrystallographic symmetry WITHIN THIS CRYSTAL
(eg 2 for twofold, 3 for threefold etc, MAX=12.
Note that it may be one if only cross-crystal
averaging of monomers is used)
MSK(1) = Mask no. identifying envelope mask for molecule 1
in this crystal
MSK(2) = Mask no. identifying envelope mask for molecule 2
in this crystal
.
.
MSK(NMOL) = Mask no. identifying envelope mask for molecule NMOL
in this crystal
Note that the mask numbers should correspond to those used during mask
creation (1-12), and refinement of the operator(s).
The following card must be repeated NMOL -1 times, with each entry
providing the operator which moves molecule 1 to each additional
NC related molecule WITHIN THIS CRYSTAL, eg for a pure threefold,
operator which moves molecule 1 to molecule 2, and operator which
moves molecule 1 to molecule 3 must be supplied, but the parameters
however, will be the same except for CHI. In that case all three
molecules may have the same mask no. Note that if nmol=1 this card
should NOT be included!
CARD(S) VII PHI, PSI, CHI, OX, OY, OZ, T (free format)
Spherical polar angles defining direction and rotational order
PHI = of noncrystallographic symmetry axis, oriented with respect to
orthogonal frame with X along a, Y along c* cross a, and Z
along x cross y (i.e. c*).
PSI = Psi = angle between NC symmetry axis and +Y axis. Phi = angle
between projection of NC symmetry axis on XZ plane and +X axis.
CHI = +Phi = CCW rotation about +Y axis as measured from +X axis.
+Chi = CW rotation about the directed axis, when viewed from
the +axis toward the origin. All angles in degrees.
OX =
Origin of NC symmetry rotation axis, in angstroms with respect
OY =
to the orthogonal axes. The axis passes through this point.
OZ =
T = Post rotation translational shift (in angstroms) parallel to the
rotation axis.
Note that the transformation operator input is defined as that which
moves molecule 1 to molecule J (both molecules within this crystal,
with J ranging from 2 to NMOL) via
Xj = (Rm) (X1 - Xo) + Xo + T*Rx
where Rm is a 3x3 rotation matrix expressed in terms of the spherical
polar angles, Xj, X1 are 3 element column vectors containing new and
old coordinates, respectively, Xo is a 3 element column vector
containing coordinates of the origin point for the rotation axis, T is
a post rotation translation shift scalar (in angstroms) and Rx is a 3
element column vector containing direction cosines of the rotation
axis.
The translation shift T is for a translation parallel to the
rotation axis (screw like) as translations in any other direction
can be achieved simply by changing the rotation axis origin. An
initial estimate of T can be obtained from two points P1, P2 related
by the NC symmetry from
T = DX cos(PHI)sin(PSI) + DY cos(PSI) -DZ sin(PHI)sin(PSI)
where DX = P2x-P1x, DY = P2y-P1y, DZ = P2z-P1z
and the P's are expressed in the orthogonal axial system.
Note the directionality of the transformation (P1 going to P2 as
opposed to P2 going to P1) affects the sign of T (and CHI).
THIS IS THE END OF INPUT UNLESS DOING CROSS-CRYSTAL AVERAGING
**** The following cards should be included ONLY if NCRYST > 1 ****
Cards VIII must be repeated NCRYST -1 times, with each entry
providing the operator which moves molecule 1 in crystal 1 to molecule
1 in crystal 2, molecule 1 in crystal 1 to molecule 1 in crystal 3,
molecule 1 in crystal 1 to molecule 1 in crystal 4 etc.
CARD(S) VIII PHI, PSI, CHI, OX, OY, OZ, T (free format)
PHI =
PSI =
All defined as described above. Note that the operator
CHI =
is applied to ORTHOGONAL coordinates in crystal 1 to
OX =
generate ORTHOGONAL coordinates in the target crystal.
OY =
OZ =
T =
NOTES: Each input mask must coincide exactly with its corresponding
input map.
CROSS-CRYSTAL AVERAGING: If the different crystals contain different
aggegation states of the molecule within their respective asymmetric
units (eg monomer in one crystal, dimer in another). Then the
crystal with the lowest agregation state should come first in the
input list, and mask assignments in the other crystals must uniquely
identify molecules of this same size. Thus for example, if a
crystal contained a dimer having pure NC twofold symmetry and it was
the only crystal used, normally a single mask encompassing the
entire dimer would be supplied (mask numbers would be identical for
molecules 1 and 2). If however, in addition to averaging over this
twofold, one also averages with another crystal form containing only
a monomer, then the monomer crystal should come first in the list,
and different mask numbers must be used within the dimer crystal
to distinguish the individual monomers. If all crystal forms contain
the same basic unit (eg dimers, trimers etc), then individual mask
numbers for each monomer are not required, but may still be used as
long as it is done consistantly in all crystals.
***** FILES *****
INPUT 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
INPUT MASK FILES (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 used (i.e. inside envelope masks 1,2,3,4,5 etc, respectively).
OUTPUT MAP FILES (BINARY)
Identical (in structure) to input map file, but contains density
"averaged" over the specified points.