uncryst (1) - generate atomic coordinates from crystallographic symmetry

UNCRYST(1)

NAME

uncryst - generate atomic coordinates from crystallographic symmetry

SYNOPSIS

uncryst [-s symmetry_description_file] [-l level] [-M] [

input_PDB_file [ output_PDB_file ] ]

DESCRIPTION

Uncryst reads a Protein Data Bank file and generates coordinates for subunits based on the crystallographic symmetry information obtained from the CRYST and SCALE records. Uncryst assumes that the input PDB file contains atoms from a single subunit, and creates a PDB file which contains multiple copies of the input atoms, with each group transformed by a symmetry operator defined by the space group definition from the CRYST record.

The -s argument specifies a file that contains the symmetry descriptions of crystallographic space groups. The format of the file is given below. If the -s option is not specified, then a default file (see FILES section) will be consulted. The -l argument specifies the output level (see below for explanation). The default output level is zero. The -M argument specifies that each matrix used to transform the coordinates be printed. In addition, the determinants of the rows and columns of the rotational part of the matrix are also printed. These numbers should all be unity; deviation from unity results in skewed coordinates for the generated subunits.

If the output PDB file argument is omitted (or given as ``-''), uncryst will write to standard output. If the input PDB file argument is omitted (or given as ``-''), uncryst will read from standard input.

SYMMETRY DESCRIPTION

The symmetry description file contains a list of space group definitions. Each space group definition consists of a set of symmetry operators, divided into levels. Each symmetry operator describes how to transform atomic coordinates in fractional crystallographic coordinates. A symmetry operator is only applied if its level is less than or equal to the output level. The following is a single space group definition: (1) spacegroup "R 3" (2) level 0 (3) x, y, z (4) -y, x - y, z (5) y - x, -x, z (6) level 1 (7) x + 1/3, y + 2/3, z + 2/3 (8) -y + 1/3, x - y + 2/3, z + 2/3 (9) y - x + 1/3, -x + 2/3, z + 2/3 (10) x + 2/3, y + 1/3, z + 1/3 (11) -y + 2/3, x - y + 1/3, z + 1/3 (12) y - x + 2/3, -x + 1/3, z + 1/3

Line 1 indicates that this is the definition for the space group named ``R 3.'' The name is used to compare against the space group symbol found in columns 56 through 66 of a PDB CRYST record. Line 2 specifies that the subsequent symmetry operators are assigned a level of zero. Lines 3, 4, and 5 are symmetry operators. Line 3 defines a symmetry operator that regenerates the input atomic coordinates (this operator is typically present). Lines 4 and 5 define two symmetry operators that generate new subunits. Line 6 specifies that subsequent symmetry operators are assigned a level of one. Lines 7 through 12 define six symmetry operators that generate new subunits.

Each symmetry operator is defined by three formulae which transform the x, y, and z coordinates respectively in the crystallographic fractional unit cell. Each formula is a simple arithmetic expression consisting of numbers, ``x,'' ``y,'' and ``z.'' Only the simple arithmetic operators are permitted. Grouping using parentheses is not supported. An additional restriction on the formulae is that they may only be linear combinations of ``x,'' ``y,'' and ``z.'' Formulae that violate this restriction are silently ignored. There can be no blank lines in a space group. Lines beginning with a ``#'' can be used to insert comments.

FILES

     /usr/local/midas/resource/uncryst.sdf       Default space
     group file

AUTHOR

Conrad Huang and Eric Pettersen

Computer Graphics Laboratory

University of California, San Francisco