ALMN

• Input file
• Output file
• Commands
• Examples
• References

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Input file

Output file

Caution

2 pi Rintegral / dmin ~ lmax (1)

Commands

The following are the available commands. The commands marked with a star (*) are mandatary to the program, and those without star are optional.

ALMN*, CELL*, FCUTOFF, HKL*, HKL_A, INCLUDE , RESOLUTION , RMORIGIN , SHELL* , SYMMETRY* and !comments.

ALMN file_name

ALMN inputs the file name of the output coefficient file.

CELL a, b, c, alpha, beta, gamma, convention_number

CELL inputs the cell parameters. The convention used to define the orthogonal (xyz) coordinate system relative to the crystal (abc) coordinate system is specified by an integer code from 1 to 8. The same code is used in the programs ROTFUN and FASTRAN. Usually, the convention used does not affect the calculation, but affects how the rotation function solution is applied to the search model. The convention codes are as follows.

	1: x//a*, y//b, z//(a* X b) -- TNT convention
	2: x//(b X c*), y//b, z//c*
	3: x//(b* X c), y//b*, z//c
	4: x//a*, y//(c X a*), z//c
	5: x//a, y//(c* X a), z//c*
	6: x//a, y//b*, z//(a X b*) -- PDB convention
	7: x//(a-b), y//(a+b-2c), z//(a+b+c) -- only for R+ lattice
	8: x//(a-c), y//(2b-a-c), z//(a+b+c) -- only for R- lattice

FCUTOFF cutoff

FCUTOFF defines the low cutoff for the structure factors. Any reflection which weaker than this will be treated as 0.0. The default cutoff is 0.0.

HKL file_name

HKL inputs the file name of the structure factors. Only unique reflections are expected. If redundant reflections are input, the first input reflection of an equivalent group will be used. For example, the current version of ALMN has the maximum number of reflections of 40,000 and the maximum absolute crystal index of 50.

HKL_A file_name, Frac

HKL_A inputs the name of the HKL/TNT file containing the structure factors of a known structural fragment. The structure factors should be calculated in the observed cell with the full symmetry of the crystal. If this option is used, the Patterson map of the known structural fragment will be subtracted from that of observed one (i.e. the one corresponding to the HKL card). Frac is the fraction of total scattering matter contributed by the fragment, which must be between 0.1 and 0.9.

INCLUDE file_name

INCLUDE defines an input parameter file, which may contain any of the input cards, including INCLUDE card itself. For example, the symmetry operators can be input from a separate file for convenience.

RESOLUTION dmin, dmax

RESOLUTION defines the resolution limits used in calculating the Al,m,n coefficients. A typical resolution shell is from 3.5 Å to 10.0 Å. Data of resolution higher than 3.0 Å is usually avoided, since the similarity between the search model and the observed crystal often becomes worse at high resolution. Meanwhile, using high resolution data will restrict the integral radius to be small.

RMORIGIN number_of_shells

RMORIGIN removes the origin peak from the Patterson map. It may help to reduce the noise in the rotation function. This is actually done by dividing the data into shells and subtracting the average intensity of the shell from the intensity of each reflection. The parameter number_of_shells defines the number of shells, into which the data within the resolution limits will be divided.

SHELL Rintegral, [Rintergral_inner]

SHELL inputs the radius of integration in Å. The radius should be chosen so that the integral sphere encloses most of the intra-molecular vectors of the search model, while excluding as many inter-molecular vectors as possible. If only one Rintergral is given, a spherical, instead of shell, integration will be used. See also formula (1) in the caution section.

SYMMETRY symmetry_operator

SYMMETRY inputs the symmetry operator in the international table format. One SYMMETRY card inputs one symmetry operator. The SYMMETRY card can be repeated up to 32 times. In the case of centered space group, only are the symmetry operators directly related to the origin is needed.

!comment

Any input line starting with a semicolon (;) or an exclamation mark (!) will be ignored.

Examples

(1) an example VAX/VMS command file to calculate the Al,m,n coefficients of a model Patterson map.

	$ RUN MRCHK_ROOT:[EXE]ALMN60
	HKL              Fmodel.HKL
	ALMN             MODEL.ALM
	; for simplicity, the cell dimensions here are the same as those for the observed.
	CELL             172. 172. 80. 90. 90. 120. 6
	SYMM             X,   Y,  Z 
	RESOLUTION       4., 8.
	RMORIGIN         8
	SHELL            24.
	$

	$ RUN MRCHK_ROOT:[EXE]ALMN60
	HKL              Fobs.HKL
	ALMN             OBS.ALM
	CELL             172. 172. 80. 90. 90. 120. 6
	SYMM             X,   Y,  Z 
	SYMM             -Y, X-Y,  Z 
	SYMM             Y-X,  -X,  Z 
	SYMM             Y,   X, -Z 
	SYMM             -X, Y-X, -Z 
	SYMM             X-Y,  -Y, -Z 
	RESOLUTION       4. 8.
	SHELL            6. 24.
	$ 

	$ RUN MRCHK_ROOT:[EXE]ALMN60
	HKL              Fobs.HKL
	HKL_A            Model_a.HKL 0.5
	ALMN             OBS-A.ALM
	CELL             172. 172. 80. 90. 90. 120. 6
	SYMM             X,   Y,  Z 
	SYMM             -Y, X-Y,  Z 
	SYMM             Y-X,  -X,  Z 
	SYMM             Y,   X, -Z 
	SYMM             -X, Y-X, -Z 
	SYMM             X-Y,  -Y, -Z 
	RESOLUTION       4. 8.
	RMORIGIN         8
	SHELL            24.
	$ 

References

2. Kabsch W. (1986) "Rotation Function" (working notes)

3. Tanaka N. (1977) Acta Cryst. A33,191-193

4. Trunrod, D., (1987). TNT refinement program package. Acta Cryst. A43, 489-503.

5. Yeates, T.O. (1989). Acta Cryst. A45,309-314

6. Zhang, X.-J. and Matthews W.B. (1994). Enhancement of the Method of Molecular Replacement by Incorporation of Known Structural Information. Acta Cryst. D50, 675-686.