CSYMMATCH (CCP4: Supported Program)

NAME

csymmatch - Apply symmetry and cell shifts to each chain in 'pdbin' to obtain the best match to 'pdbin-ref'

SYNOPSIS

csymmatch -pdbin-ref filename -pdbin filename -pdbout filename -connectivity-radius radius/A -origin-hand [-stdin]
[Keyworded input]

DESCRIPTION

'csymmatch' will move chains in file 'pdbin' to match as far as possible chains in file 'pdbin-ref', using symmetry operations and allowed origin shifts to generate the best fit. The shifted coordinates are written out in 'pdbout'.

Note that this is not a structural superposition. 'csymmatch' only uses a fixed set of symmetry-related transformations.

It makes an intelligent guess based on chain ID and proximity as to what is a contiguous unit in the file, and moves on that basis. Separate chains are always moved separately. Monomers within a chain which do not have close contiguity to their neighbours - e.g. waters, broken chains - are also moved separately.

INPUT/OUTPUT FILES

-pdbin-ref

Input PDB file containing the reference structure.

-pdbin

Input PDB file containing the coordinates to be shifted.

-pdbout

Output PDB file containing the shifted coordinates.

KEYWORDED INPUT

See Note on keyword input.

-connectivity-radius radius

Default: 2.0 A
Radius (in Angstrom) used to determine which fragments form a contiguous unit, to be moved together.

-origin-hand

Also try all possible origin shifts, and changes of hand.

Note on keyword input:

Keywords may appear on the command line, or by specifying the '-stdin' flag, on standard input. In the latter case, one keyword is given per line and the '-' is optional, and the rest of the line is the argument of that keyword if required, so quoting is not used in this case. End input with <Ctrl-D> (END is not recognised).

Program Output

The program reports any change of hand, or origin shift used (which is applied to the entire contents of 'pdbin'). It then outputs the symmetry operation and lattice shift used for each chain identified in 'pdbin'.

It also outputs a normalised score for each positioned chain, which is the average map value at the atoms of that chain. The map in question is calculated from the reference structure. A well positioned chain will tend to overlap the reference map, and lead to a higher score (closer to 1.0).

Problems

One limitation: Without -origin-hand it doesn't try origin shifts. With -origin-hand it tries all possible origin shifts, not just those consistent with the spacegroup symmetry. Normally the symmetry of the search target wins out and you get an exact answer, but with very poor models it can occasionally give garbage.

AUTHOR

Kevin Cowtan, York.

SEE ALSO

reforigin, solution_check (Balbes)