PEAKMAX (CCP4: Supported Program)
NAMEpeakmax - search for peaks in the electron density map
SYNOPSISpeakmax MAPIN foo_in.map [XYZOUT foo_out.pdb] [XYZFRC foo_frac.out] [PEAKS foo_peak.out]
DESCRIPTIONSearch map (in standard map format) and list coordinates of all peaks (optionally all positive peaks only) with height above a given threshold. The peaks are listed in grid, fractional and orthogonal coordinates, in the order they are found in the map and sorted in descending order of absolute value of peak height. The list of peaks is checked for symmetry-related peaks, and these are assigned a unique site number to indicate which peaks are related. A peak list can be written to output files: in a format with fractional coordinates suitable for input to MLPHARE and/or to a PDB file for further processing, e.g. with WATPEAK or graphics program such as O.
The various data control lines are identified by keywords, those available being:
ATNAME, BFACTOR, CHAIN, NUMPEAKS, ORTHOGONALIZATION, OUTPUT, PATTERSON, RESIDUE, THRESHOLD, XYZLIMIT, END
THRESHOLD [RMS] <threshold> [NEGATIVES][default THRESHOLD RMS 3]
Threshold for peaks: all peaks with values above <threshold> will be selected.
OUTPUT [ PDB | FRAC | PEAKS | NONE ][default OUTPUT PDB]
By default, output PDB files contain in the occupancy column, the peak height, and in the Bfactor column, height/rms(density). If the BFACTOR command is present, these columns will be set to occupancy & Bfactor. Note that one or more of the subkeywords - other than 'NONE' - can appear on the same line as the OUTPUT keyword; they are not mutually exclusive.
BFACTOR <Bfactor> [<Occupancy>][default: set occupancy = peak height/rms(density), Bfactor = height]
Define Bfactor [& occupancy] for output file.
RESIDUE <Residue_type>[default HOH]
Set residue type for output file.
ATNAME <Atom_name>[default O]
Set atom name for output file.
CHAIN <Chain_ID>[default X]
Set chain identifier for output file
NUMPEAKS <nop>(<= 8000) (Default: 800)
Number of peaks to output in the list, sorted by height
ORTHOGONALIZATION <Ncode>[Default: 1 (Standard PDB)]
Set orthogonalisation convention
=1 A // XO, C* // ZO (Standard PDB) =2 B // XO, A* // ZO =3 C // XO, B* // ZO =4 HEX A+B // XO, C* // ZO =5 A* // XO, C // ZO (Rollett)
PATTERSONIf given then the patterson vector lengths will be given for the sorted list. If there is possible NCS translation the output is flagged.
***** NCS translation likely ***** Origin peak: 337.21 0.000 0.000 0.000 0.00 0.00 0.00 Possible NCS Peak, fractional & Orthogonal coords 79.76 0.209 0.000 0.490 19.45 0.00 34.09
XYZLIMIT <NU1> <NU2> <NV1> <NV2> <NW1> <NW2>[Default: If this keyword is omitted, the whole map is searched]
Limits for search in grid units on fast, medium, slow axes.
INPUT AND OUTPUT FILES
OutputWhich of the following output files (if any) are produced depends on the values of the subkeywords given with the OUTPUT keyword. In all cases the height/(rms density) is written for each peak (i.e. not the "absolute" peak height)
NOTESIn the PDB file on stream XYZOUT, the peaks are put out as waters with a chain identifier of X until residue 999 is reached, when the sequence continues from 1 and chain id Y. The official PDB format allows the residue number to contain up to four digits, so this is technically unnecessary.
SEE ALSOThe program WATPEAK can be used to associate the peaks/holes with atomic coordinates from the output with OUTPUT PDB (default options).
Contact: Phil Evans (6-OCT-1989 12:33) Email : PRE@MRC-MOLECULAR-BIOLOGY.CAMBRIDGE.AC.UK (email@example.com) Other authors: Ian Clifton (30-Jul-1993) Address: Laboratory of Molecular Biophysics Oxford University Rex Richards Building South Parks Road Oxford OX1 3QU UK Phone: +44 865 275387 Email (INTERNET): firstname.lastname@example.org Email (X.400): C=GB;ADMD= ;PRMD=UK.AC;O=OX;OU=BIOP;S=Ian
Simple unix example scripts found in $CEXAM/unix/runnable/
vms versions found in $CEXAM/vms/