HEAVYTRAN

HEAVYTRAN calculates a translation function, H-translation function, based on the data of one heavy-atom derivative [2]. The {(|Fo,der.(h)| - |Fo,nat.(h)|) / |Fo,nat.(h)|} and the corresponding coordinates, X0, of the heavy-atom site(s) are required. This version of HEAVYTRAN uses Fast Fourier Transform. The equation used by HEAVYTRAN is sensitive to the weak reflections of Fo,nat.. Therefore, excluding weak reflection, say 25%, may improve the effectiveness of the equation. The H-translation function is defined by the following Equations.

Eq. 1.  HT( t )   =  sum[ (Fc(h, t ) exp( -i2pihX0 ) |Fo,der.(h)| - |Fo,nat.(h)|) 
                               / |Fo,nat.(h)|  ] / v
Eq. 2.  Fc(h, t ) =  sum[ TFc,m(Sh) ] 
                  =  sum[ Fc,m(hR) exp( i2pihT +i2pihRt )

where {Sj(Rj,Tj), j=1,nsym} are the symmetry operators of the crystal and their rotation-translation components, T is a translation operator corresponding to a translation t in real space, Fc,m's are structure factors calculated with the single search model, and v is the volume of the crystal unit cell.

Input file
Output file
Commands
Examples
References

To report bugs, please contact

Cai X.-J. Zhang at chk@uoxray.uoregon.edu

Input files

Two structure factor files of HKL/TNT format are expected as the input.

Output file

The output file is a HKL/TNT format file containing the coefficients for making the map of HT( t ).

Commands

HEAVYTRAN uses key-word leading, free format input cards. A key-word can be abbreviated as long as there is no ambiguity caused.

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

CELL*, FC*, FO*, HEAVY*, INCLUDE, RESOLUTION*, SYMMETRY*, HT_C* and !comment.

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

CELL inputs the cell parameters in Angstroms and degrees.

FC file_name

FC defines the HKL/TNT file name of the calculated structure factors. When the {Fc} are calculated, the model cell should be the same as the crystal cell with a unitary symmetry, plus any centering operation. The model should be at a correct orientation (i.e. the solution of the rotation function).

FO file_name

FO inputs the HKL file name of the {|Fo,der.(h)| - |Fo,nat.(h)|} structure factors. The phases of these structure factors should be either 0.° or 180.°.

HEAVY x_frac, y_frac, z_frac, weight

HEAVY defines the positions of the heavy atom sites. There should be one HEAVY card for each heavy-atom site.

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 of both {Fo} and {Fc} used in the calculation.

SYMMETRY symmetry_operator

SYMMETRY inputs the symmetry operator in the international table format. For a centered space group, only the symmetry operators associated with one origin are needed. The origin shifts should be included in the structure factor calculation.

HT_C file_name

HT_C defines the name of the output coefficient file.

!comment

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

Examples

The following example is of the E.coli Methionine Aminopeptidase (Roderick and Matthews, 199x). The space group is P21. There is one molecule per asymmetric unit.

	$ run mrchk_root:[exe]heavytran
	cell       39.0 61.7 54.5 90.0 107.3 90.0
	resolution 4., 10.
	symmetry   X,   y,  z 
	symmetry   -x, y+1/2,  -z 
	fo         pb-nat.Hkl
	fc         fmodel.Hkl
	heavy      0.9972    1.0281    1.2246  1.0
	heavy      1.0110    0.9650    1.1842  0.8
	Ht_c       ht.map
	$
	$ run tnt_util:Fourier
	cell       39.0 61.7 54.5 90.0 107.3 90.0
	resolution 4., 10.
	File       ht_c    ht.hkl   Format hkl
	punch ht.Map map source ht_c  grid 40 60 50 layout 0 40 0 60 0 50
	$

The solution may be sensitive to the accuracy of the coordinates of the heavy-atom sites. In other words, the accuracy of the solution will not be better than the accuracy of the heavy- atom site(s). A wrong set of coordinates of the heavy-atom sites might result in a wrong resolution which appeared as a good one.

References

1. Tronrud, D., et.al. (1987). TNT refinement package. Acta Cryst. A43, 489-503.

2. 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.