PEKCHK

PEKCHK searches peaks in a Ten Eyck format map file (Ref. TNT refinement package).

To report bugs, please contact

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

Input file

One or two Ten Eyck format map file(s) are expected as the input. The format has been modified to accept non-unitary step size.

Output file

PEKCHK creates a PDB format coordinate file to store the gridding coordinate of the peaks. The coordinates are determined using quadratic interpretation. The peak height at nearest lattice point can also be reported as required.

Commands

PEKCHK 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.

B_FIELD, GRID, INCLUDE, MAP*, MAP_B, PERMUTE, PUNCH, SCALE, STEP, TOP, W_FIELD and !comment.

B_FIELD {MAP_A, SGM_A, MAP_B, SGM_B}

B_FIELD defines the content of the B-field (of PDB format) of the output list of the peaks. For example, the MAP_A option, which is the default, reports peak value in map A. Other options include: SGM_A reports peaks in terms of the standard deviation (from zero) of map A; MAP_B reports value of map B at the peak position of map A; and SGM_B reports value of map B in terms of its standard deviation (from zero) at the peak position of map A.
GRID x_grid, y_grid, z_grid
GRID defines the gridding along the x, y, z axes. It overwrites the gridding information in the Ten Eyck map file.
INCLUDE file_name
INCLUDE defines an input parameter file, which may contain any of the input cards, including INCLUDE card itself.
MAP map_file_name
MAP or MAP_A inputs the file name of the principal map which has the Ten Eyck format. Peaks are searched in this map.
MAP_B map_file_name
MAP_B inputs the file name of a secondary map which has the Ten Eyck format. While the peak search is based on map A, the value of map B at the peak position can be monitored as required.
PERMUTE fast_id, slow_id, section_id
PERMUTE defines the input order of the map file. For example, for a map of X cross (fast), Y down (slow) and Z section, the order is (1, 2, 3), which is the default. For a map of Z cross, X down and Y section, the order is (3, 1, 2).
PUNCH pdb_file_name
PUNCH defines the file name of the output peak list. The default is SYS$OUTPUT, eg. the .log file for a batch job.
SCALE scale_a, [scale_b]
The value in the input map files A and B will be multiplied by the corresponding scale . The default is 1.0. All the statistics of the map is based on the map after scaling.
STEP step_x, step_y, step_z
STEP inputs the increments of the three-dimensional lattice in grid units. The default is (1, 1, 1). If the input is different from (1, 1, 1), the input map file is not a standard Ten Eyck map file.
TOP number_of_peaks
TOP defines the number of peaks to be listed. The default is 100.
W_FIELD {MAP_A, SGM_A, MAP_B, SGM_B}
W_FIELD defines the content of the W-field (of PDB format) of the output list of the peaks. For example, the SGM_A option, which is the default, reports the peak value in map A in terms of its standard deviation. See also B_FIELD.
!comment
Any input line starting with a semicolon (;) or an exclamation mark (!) will be ignored.

Examples

(1) an example VAX/VMS command file to search peaks in a rotation function map. 
	$ RUN PEKCHK_EXE:PEKCHK
	TOP        500
	PERMUTE    3,  1, 2
	STEP       3,  3, 3
	MAP        rotfun.map
	PUNCH      peak_list.pdb
	$
(2) an example VAX/VMS command file to search the top 20 peaks in a translation function map. 
	$ RUN PEKCHK_EXE:PEKCHK
	TOP        20
	MAP        fastran.map
	$
(3) an example VAX/VMS command file to search the top 20 peaks in a translation function map while monitoring an overlap function. 
	$ RUN PEKCHK_EXE:PEKCHK
	TOP        20
	MAP        fastran.map
	MAP_B      overlap.map
	W_FIELD  sgm_a
	B_FIELD    sgm_b      
	$
Copyright 1995, Cai X.-J. Zhang, All Right Reserved.