PEAKMAX (CCP4: Supported Program)
- search for peaks in the electron density map
Search 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
ATNAME, BFACTOR, CHAIN, EXCLUDE, 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.
peaks will be chosen if they are more than <threshold> * (rms density),
instead of an absolute value.
negative peaks below -<threshold> will be selected as well as positive
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
- PDB (default)
write sorted peaks to a PDB format coordinate file with
logical name XYZOUT
write sorted peaks with fractional coordinates to the file with
logical name XYZFRC, in a format suitable for input to MLPHARE.
N.B.: In OUTPUT FRAC, no file will be written if the
PATTERSON keyword is also present.
write unsorted peaks file to logical name PEAKS
no output file
BFACTOR <Bfactor> [<Occupancy>]
[default: set occupancy = peak height/rms(density), Bfactor = height]
Define Bfactor [& occupancy] for output file.
Set residue type for output file.
Set atom name for output file.
Set chain identifier for output file
(<= 8000) (Default: 800)
Number of peaks to output in the list, sorted by height
[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)
If 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.
EXCLUDE [ EDGE | NONE ]
[Default: EXCLUDE EDGE]
Attempt to suppress output of symmetry-equivalent peaks at the map
edges (EXCLUDE EDGE), otherwise output all peaks (EXCLUDE NONE). It
should be noted that EXCLUDE EDGE doesn't always successfully
suppress all the equivalent peaks.
INPUT AND OUTPUT FILES
Map file to be searched for peaks, in CCP4 map format.
Which 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"
Sorted list of peaks written in PDB format; produced when the
OUTPUT PDB option is specified.
See also the NOTES below.
Sorted list of peaks with fractional coordinates in a format
suitable for input to MLPHARE; produced with the OUTPUT FRAC option.
No file will be written if the
PATTERSON keyword has been specified.
List of unsorted peaks produced when the OUTPUT PEAKS option is specified.
In 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
The program WATPEAK can be used to associate the
peaks/holes with atomic coordinates from the output with OUTPUT PDB
Contact: Phil Evans (6-OCT-1989 12:33)
Email : PRE@MRC-MOLECULAR-BIOLOGY.CAMBRIDGE.AC.UK
Other authors: Ian Clifton (30-Jul-1993)
Address: Laboratory of Molecular Biophysics
Rex Richards Building
South Parks Road
Oxford OX1 3QU
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/
(calculating a 3Fo - 2Fc map)
(calculating an Fo-Fc map)
(A simple Procedure for finding water peaks)
(Procedure for finding water peaks.)