PACKCHK

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

To report bugs, please contact

Input files

Output file

Commands

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

CELL, DELTA, GRID*, INCLUDE, LAYOUT, PDB_IN*, PUNCH*, SYMMETRY* and !comment.

CELL card defines the cell parameters. A CELL card will overwrite the cell parameters read from the input PDB file if exiting. The default is that defined in the input PDB file. 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 by other programs in this package. 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

DELTA defines the distance cutoff for the bad-contact search. delta is the maximum distance in Å for a pair of atoms to be considered as having bad- contact. The larger the delta is, the more lattice points will be marked as intolerable (with a value 0.0 in the output map). max_contact defines the maximum number of tolerable bad-contacts. At a given position if the number of bad-contacts exceeds max_contact, the corresponding lattice point will be labeled as intolerable. The default is ( 4.0, 1), which is usually good for a C-alpha backbone search model.

GRID defines the gridding along the three crystallographic axes. Usually the a_grid, b_grid and c_grid should match that of the translation function map.

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.

LAYOUT card defines the layout of the output map in grid units (which are defined by the GRID card). The default layout is ( 0, a_grid - 1 ; 0, b_grid - 1 ; 0, c_grid - 1 ).

PDB_IN defines the name of the input PDB file. Usually the file contains a header describing the cell parameters and the alignment. For a protein molecule, the C-alpha atoms alone are usually sufficient (and efficient) for the packing calculation.

PUNCH defines the name of the output Ten Eyck map file [2] that contains the overlap function.

SYMMETRY card inputs symmetry operators in the international table format. There should be one SYMMETRY card for each symmetry operator.

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

Examples

	$ run mrchk_root:[exe]packchk
	pdb_in    ca.pdb
	cell      61.2,  61.2,  96.8,  90,  90,  120, 6
	grid 	  64,  64,  96
	layout    0  63,  0  63,  0 47
	include   p3221.dat
	punch     pack.map
	delta     4.0  1
	$ 

	symm x,y,z
	symm -y,x-y,z+2/3
	symm y-x,-x,z+1/3
	symm y,x,-z
	symm -x,y-x,-z+2/3
	symm x-y,-y,-z+1/3

	$ run mrchk_root:[exe]pekchk
	! search peaks in the fast translation function map
	map_a   t.map
	
	! monitor the overlap function map
	map_b   pack.map

	! list the peaks in the translation function map, t.map
	b_field sgm_a
	! report the overlap function value at the peak positions.
	w_field map_b

	top 50
	$

References

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