PEAKMAX (CCP4: Supported Program)

NAME

peakmax - search for peaks in the electron density map

SYNOPSIS

peakmax MAPIN foo_in.map [XYZOUT foo_out.pdb] [XYZFRC foo_frac.out] [PEAKS foo_peak.out]
[Keyworded input]

DESCRIPTION

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.

KEYWORDED INPUT

The various data control lines are identified by keywords, those available being:

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.
Subkeywords:
RMS
peaks will be chosen if they are more than <threshold> * (rms density), instead of an absolute value.
NEGATIVES
negative peaks below -<threshold> will be selected as well as positive peaks.

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.
Subkeywords:
PDB (default)
write sorted peaks to a PDB format coordinate file with logical name XYZOUT
FRAC
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.
PEAKS
write unsorted peaks file to logical name PEAKS
NONE
no output file

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)

PATTERSON

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.

END

End input.

INPUT AND OUTPUT FILES

Input

MAPIN
Map file to be searched for peaks, in CCP4 map format.

Output

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" peak height)
XYZOUT
Sorted list of peaks written in PDB format; produced when the OUTPUT PDB option is specified.
See also the NOTES below.
XYZFRC
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.
PEAKS
List of unsorted peaks produced when the OUTPUT PEAKS option is specified.

NOTES

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 unnecessary.

SEE ALSO

The program WATPEAK can be used to associate the peaks/holes with atomic coordinates from the output with OUTPUT PDB (default options).

AUTHOR

Contact:   Phil Evans (6-OCT-1989 12:33) 
  Email :  PRE@MRC-MOLECULAR-BIOLOGY.CAMBRIDGE.AC.UK
    (pre@mrc-lmb.cam.ac.uk)

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):  ian@biop.ox.ac.uk
  Email (X.400):  C=GB;ADMD= ;PRMD=UK.AC;O=OX;OU=BIOP;S=Ian

EXAMPLES

Simple unix example scripts found in $CEXAM/unix/runnable/

  • 3fo2fcmap (calculating a 3Fo - 2Fc map)
  • fofcmap (calculating an Fo-Fc map)
  • watpeak.exam (A simple Procedure for finding water peaks)
  • waterpeaks (Procedure for finding water peaks.)