REFLECTION commands manipulate reflection data and structure factors. They are used for proper scaling and structure factor manipulation including an R-VALUE calculation that finally leads to FILL-MAP and its FOURIER BACK TRANSFORM.
There are three data structures FOBSERVED, FCALCULATED and FWORKSET that can be manipulated with REFLECTION commands. FOBSERVED are usually amplitudes of a measured data set (read from a file), FCALCULATED array is automatically filled with a MAP FOURIER transformation, FWORKSET is used to prepare a map (wirh FILL-MAP command) for FOURIER map BACK transformation.
> REFLECTION
EXIT
EXPAND
FILL-MAP inte
KEY string SELECT ... END
MOVEFCFO
KICK (
= real
SEED
LINEAR
SQUARE
EXPONENT
)
PHASES STATISTICS
FROM FOBS
TO FCALC
FWORK
SAYRE-EQ
R-VALUES TEMPERAT real
B-WILSON
RESOLUTION real real
SELECT ... END
SET AMPLITUDE
PHASE
SCALE FOBSERVE expresion + - * / expresion
FCALCULA
FWORKSET
expresion as FOBSERVE * ^ / real
FCALCULA
FWORKSET
SHELLS inte
SHOW KEYS
TWINS
REFELCTIONS
SOLV_FLAT real
SYMMETRY inte inte
WEIGHTS CONSTANT
SIGMA
A_SIGMA real
R-VALUES
... EXPAND FCALCULATE
FOBSERVED
FWORKSET
EXPANDS specified structure factors applying SYMMETRY operators in specified RESOLUTION range to the HKL limits as generated by the last READ REFLECT INIT command.
... FILL-MAP inte
Specifies a complex map that will be filled with structure factors form the WORKSET as a preparation step for a following FOURIER (FFT) map BACK TRANSFROM.
... KEY string SELECT ... END
INITIALIZE
DROP
A selected set of structure factors can be addressed using a KEY name in consequent REFLECTION commands. It is an analogue of atom selections KEY.
... KICK (
= real
SEED inte
LINEAR
SQUARE
EXPONENT
)
FCALC are kicked inside the given kick value (maximum distance) which has a LINAR (resol * kick), SQUARE (resol**2
dependance from resolution.* kick) or EXPONETIAL ( k * exp(-resol**2 * B) * kick)
Centric reflections are kicked only along real or imaginary componet, whereas the noncentric reflactions are kicked randomly.
Moves the curent values of FCALC into FOBS (real and imaginary part).
... PHASES (
STATISTICS FROM FOBS
TO FCALC
FWORK
SHIFT
SAYRE-EQUAT
)
STATISTICS is used for comparison of phases between two structure factor sets
> refl phase ( stati from fobs to fcalc )
The rest is not working yet.
... R-VALUES TEMPERAT real
B_REFINE
RESCALE
FIXED
Linear R-VALUE matches are calculated between FOBSERVED and FCALCULATED for the number of specified reflection shells.
Each resolution obtains independent scaling factor (K). Once they are calculated you can turn the default RESCALE of with the FIX keyword and calculate an R-FREE value:
> refle select .not TEST end r-val rescale > refle select TEST end r-val fix
A resolution dependent TEMPERATURE factor can be set or refined (B_REFINE is the default). Use at least 3 shells to get a reasonable B-value.
... RESOLUTION real real
RESOLUTION can limit any of the REFELCTION operations to a limited resolution range, however, the resolution range of reflections can not be expanded beyond the resolution limits set at the beginning (within a READ REFLECTION) sentence.
A yet more flexible way is to use SELECT commands.
... SELECT ... END
Use of () and logical operators (.AND., .NOT., .OR.) between tags is allowed.
Tags define whether a particular reflection should be chosen or not.
Select all reflections.
Select only centric reflections.
Select only defined reflections (FOBS are not zero).
... FCALC real real
Select reflections with their FCALC in a range of their amplitudes.
... FOBS real real
Select reflections with their FOBS in a range of their amplitudes.
... FWORK real real
Select reflections with their FWORK in a range of their amplitudes.
... H_INDEX inte inte
Select reflections with their H-INDEX within the given interval. When only one integer is given, the second is equal to the first one. The command
> refl select h-index 4 .and. k-index 3 .and. l-index 2 end
will select the reflection with HKL values 4,3,2.
... K-INDEX inte inte
Select reflections with their K-INDEX within the given interval. When only one integer is given, the second is equal to the first one.
... L-INDEX inte inte
Select reflections with their H-INDEX within the given interval. When only one integer is given, the second is equal to the first one.
... MODUL inte inte
Selects among defined reflections by modul and remainder. For example
> refl select modul 12 3 end
selects the 3rd 15th and so forth refelctions.
... MULTIPLI inte inte
Selects reflections within a given mulitplicity range. When only one integer is specified, the second one becomes equal to the firts one.
Selects noncentric refelctions.
... R-VALUES real real
Select reflections in a given R-VALUE range.
... RANDOM int1 int2
Select randomly among defined reflections a partition (int1) with a given seed (int2). Default int1 value is 12 and default int2 (seed) is variable RAN_SEED.
> key TEST select random 12 end
... RESOLUTION real real
Select reflections in a given RESOLUTION range.
... SHELL inte inte
Select reflections within given SHELLS. When only one integer is given, the second becomes equal to the first one.
... SIGMA real real
Select reflections with the given AMPLITUDE/SIGMA values ratio range.
Selectc UNDEFINED reflections (not read FOBS).
... AMPLITUDE
PHASE
SCALE FOBSERVE expresion + - * / expresion
FCALCULA
FWORKSET
expresion as FOBSERVE * ^ / real
FCALCULA
FWORKSET
SET commands enables you to perform various structure factor calculations that are a basis for density map calculations: Either as difference maps (Fwork = Fobs*2. - Fcalc*1, Fobs*1. - Fcalc*1.), Patterson maps (Fwork = Fobs^2.), correlations maps (for the fast solvent flattening procedure (Fwork = Fcal * 1.0 * Fwork * 1.), fast translational search etc...)
You can set AMPLITUDE, PHASE or AMPLITUDE and PHASE.
Any of reflection arrays (FOBSERVED, FCALCULATED or FWORK) can be SCALED in accordance with the constants obtained by the last R-VALUES calculation. FOBSERVED array is divided with the constants while the FCALCLATED and FWORKSET arrays are multiplied with them.
The current WEIGHTS for FOBS and FCALC are applied. Default values are one, but you can also read WEIGHTS of FOBS with PHASES to calculated a figure of merit map.
... SHELLS inte
Specifies number of SHELLS that are used in a R-VALUE calculation and in a REFLECTION SET calculation (when SCALING an data array).
... SYMMTERY inte (inte)
Can limit a FILL-MAP command to apply only the specified symmetry operations. By default all symmetry operations are used.
... SOLV_FLAT real
Sets Fcalc to the values for Fast solvent flattening based on Leslie, Acta Cryst. (1987) A43, 134-136.
... WEIGHTS CONSTANT
SIGMA
A_SIGMA real
R-VALUES
Not perfect yet. So use CONSTANT to switch from a Figure of Merit (FOM) weights obtained by reading a reflection file to constant weights. Sigma A values are only estimated and not refined.
... KEYS
TWINS
REFELCTION
... ON
OFF
MATRIX 9 * real
INITIALIZE