PROFESSS (CCP4: Supported Program)

NAME

professs - determination of NCS operators from heavy atoms

SYNOPSIS

professs XYZIN foo.pdb [XYZOUT bar.pdb] [Keyworded input]

DESCRIPTION

'professs' is a tool to help in the identification of NCS related atoms from a list of heavy atom positions. It is easier to use than 'distang', which does not assemble atoms into triangles or output the symmetry related atoms. It is less easy to use than 'findncs', but unlike that program it runs extremely quickly.

'professs' takes as input a PDB file containing the heavy atom sites. From this list, crystallographic symmetry equivalents are generated. The extended list is searched for triangles of 3 atoms, with all the spacing less than a cutoff distance (see DISTANCE keyword). The results are tabulated, so that the user may identify equivalent triangles belonging to NCS related molecules.

It then goes on to work out the operators relating pairs of triangles. Additional atoms obeying the same operators are added to the list over several cycles. The related atoms are then reduced to a common basic set so that the operators can be compared without the confusing effects of crystallographic symmetry. Any 'loops' within the resulting groups, associated with proper NCS, are listed.

A PDB file may optionally be output, containing the atoms of the triangles, with each triangle given a different chain ID. This file may be fed into 'lsqkab' for determining the operators relating the original triangles. This is only intended for tutorials, or if everything else breaks.

INPUT/OUTPUT FILES

XYZIN: Input PDB file containing the heavy atom positions. If the CRYST1 keyword is present in the file, this will also provide the unit cell dimensions, and possibly the spacegroup.
XYZOUT (OPTIONAL - ONLY FOR MANUAL OPERATION WITH DISTANG): Output pdb file containing triangles of atoms, grouped for input to 'lsqkab' Each triangle is given a separate chain ID, and each atom within the triangle is numbered, 1, 2 or 3. The atom order is chosen such that the distances are ranked d₁₂ < d₂₃ < d₃₁. (If the differences in the distances are less than the distance tolerance - an isosceles triangle - then both orderings are produced.)

KEYWORDED INPUT

CELL, SYMMETRY, DISTANCE, TOLERANCE, TIDYINPUT, VERBOSE, END.

CELL <a> <b> <c> <alpha> <beta> <gamma>

Unit cell parameters. Override the cell parameters given in XYZIN.

SYMMETRY <spacegroup_name>

Space group symmetry. Override the spacegroup given in XYZIN.

DISTANCE <distance>

Maximum interatomic distance for analysis in Angstroms. Atom pairs further apart than this distance will be ignored.

TOLERANCE <tolerance>

Tolerance on interatomic distances in Angstroms. Distances differing by less than this distance will be considered equal. This is useful when triangles are approximately isosceles or equilateral, in which case the atom order will be ambiguous. Specifying a tolerance will cause all equivalent triangles to be produced.

The tolerance is used in the second stage to choose which atoms will be included into the match sets. After determination of the operators, atom pairs within this distance will be added to the list

Try 1-3 Angstroms, depending on the quality of your heavy atom positions. Default = 1.0.

TIDYINPUT [FRAC <uc> <vc> <wc>] [ORTH <xc> <yc> <zc>]

Tidy up the input coordinates to place them close to the specified coordinate. This occurs before the rest of the calculation. Symmetry and cell numbers in the log file will refer to the tidied coordinates. If the keyword is given without a coordinate, then the atoms will be placed close to the origin with slight preference for the positive octant.

VERBOSE

Generate a few extra diagnostics.

END

End input.

Reading the Ouput:

The program first lists the triangles of atoms which it has found, then it analyses each pair of triangles as a possible NCS match. For each possible operator, a list of all matching atoms is given. For each pair of atoms, a 'loop factor' is listed. If the NCS operator is an N-fold rotation, the atom will be part a 'loop' of N atoms (unless one is missing). This, along with an appropriate 3rd polar angle, can confirm the existance of a proper NCS operator.

Atoms are described by the atom serial number from the input PDB, along with 4 numbers listed in square brackets. The first of these is the number of the crystallographic symmetry operators, and the other three are the unit cell translations applied after the symmetry operator.

Problems:

When calculating the distance between a pair of atoms, all symmetry equivalents are considered, but only the cell repeat giving the least distance is considered. In a very few cases of low order crystallographic symmetry this may cause atoms to be missed.

AUTHOR

Kevin Cowtan, York (originally named 'eleanorinabox').