COORDCONV (CCP4: Supported Program)

NAME

coordconv - Interconvert various coordinate formats

SYNOPSIS

coordconv xyzin foo_in.xyz xyzout foo_out.brk
[Keyworded input]

DESCRIPTION

This program converts various coordinate formats. It reads cell dimensions and orthogonalises the coordinates.

KEYWORDED INPUT

The data control lines are identified by the following keywords. Only the first 4 letters of each keyword are necessary.

CELL, END, INPUT, OUTPUT

INPUT [ FRAC | HA | PDB | SHELX-F | SHELX-S | CSD | XPLOR/CNS | SNB ] [ ORTH <ncode> ]

Defines the input coordinate format. The following options are supported:

FRAC

FRACTIONAL - York traditional fractional, a precursor to PDB format, e.g.

    1   0.46204   0.16203   0.02100   0.00000 0.49   16         1SE1  DER A1
    7   0.22003   0.16304   0.10299   0.00000 0.49   16         2SE2  DER A1
 Atno    Xfrac     Yfrac     Zfrac     Bfac   Occ    Atomno  IresAtnamResnm ChnnamIS

in Fortran format (I5,4F10.5,F5.2,I5,I10,A4,1X,A4,A1,I2). Note that the trailing integer after Chnnam is only output in XPLOR/CNS format PDB files.

HA

HA - the format used for CCP4 Interface input and output from MLPHARE. There is no fixed format except that any CELL information must be on a line beginning CELL, and coordinates on lines beginning ATOM. If the CELL line is given, this is used for coordinate conversion. All other lines are ignored. e.g.

    
DERIV     infl to rm
DCYCLE PHASE ALL REFCYC ALL KBOV ALL
RESO      14.76      1.56
SCALE    FPH1    0.9898   -0.0708
ISOE        5.59    5.97    7.28    6.86    6.81    7.59    8.07   11.11
RESO ANO       14.76    1.56
ANOE        2.49    3.72    4.49    4.92    5.77    7.16    8.42    8.73
ATOM1   Ano  -0.762 -0.141 -0.861  6.571  1.905 BFAC   12.603
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM2   Ano  -0.750 -0.313 -0.636  6.239  1.954 BFAC   12.981
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM3   Ano  -0.207 -0.376 -0.649  6.147  1.854 BFAC   12.216
Key    Atnam  Xfrac  Yfrac  Zfrac  Occ    ????          Bfac   

Or: 

GRID  44  50  64
CELL   47.4870   49.4897   64.5144   94.6264  109.6226   90.9455
ATOM    Ano   0.0000  0.0000  0.0000
ATOM    Ano  .471143 .315582  .197912  
ATOM    Ano  .323707 .308963  .152872  
ATOM    Ano  .257966 .781764  .924197  
ATOM    Ano   0.0145  0.3617  0.3200  
ATOM    Ano   0.8716  0.2215  0.9305  
ATOM    Ano  0.4021 0.7929   0.9775 
ATOM    Ano  0.3686 0.42450  0.1205

PDB

BROOKHAVEN with or without CRYST1 and SCALEx cards

SHELX-F

SHELX `full' (2 lines per atom)

SHELX-S

SHELX `short' (1 line per atom) e.g. a shelx.res or shelx.ins file. The format used is FORMAT(A4,I3,3F8.4,F10.6,F6.2) which corresponds to SHELXS-90. This definitely won't work with SHELXD output, but you should be able to get PDB files directly in that case.

CSD

Cambridge structural data base

XPLOR

Brookhaven - X-PLOR version. You will have to split chains later and correct some atom names. See also `OUTPUT XPLOR' option in PDBSET.

SNB

ShakeNBake peaks file in Fortran format:

(3F10.0,F10.2,I5,I2)

The peak height is assigned to the B-factor column, and the flag indicating whether the peak should be used is converted to an occupancy. The choice of input format corresponds to the format written by BnP, `The Buffalo and Pittsburgh Interface combining SnB and Phases' - see http://www.hwi.buffalo.edu/BnP/ for more information.

The ORTH keyword must be followed by <ncode> - the orthogonalisation code. The default is orthogonalisation code 1. If the INPUT is a PDB file with CRYST1 and SCALEx cards, then the SCALEx matrices override the orthogonalisation code.

      ncode = 1 -  orthogonal axes are defined to have
                   A parallel to XO   CSTAR parallel to ZO
      ncode = 2 -  orthogonal axes are defined to have
                      B parallel to XO   ASTAR parallel to ZO
      ncode = 3 -  orthogonal axes are defined to have
                      C parallel to XO   BSTAR parallel to ZO
      ncode = 4 -  orthogonal axes are defined to have
                    HEX A+B parallel to XO   CSTAR parallel to ZO
      ncode = 5 -  orthogonal axes are defined to have
                    ASTAR parallel to XO   C     parallel to ZO
      ncode = 6 -  orthogonal axes are defined to have
                      A parallel to XO   BSTAR parallel to YO

OUTPUT [ FRAC | HA | PDB | XPLOR ] [ ORTH <ncode> ]

Defines output coordinate format as above.

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

Cell dimensions in Angstroms and degrees. Angles default to 90. Compulsory unless the input file is a PDB file with CRYST1 card or an HA file with CELL specified.

END

Ends input.

INPUT AND OUTPUT FILES

XYZIN Input coordinates

XYZOUT Output coordinates

AUTHORS

Originator : Eleanor Dodson, University of York

EXAMPLES

Sample Unix input file:

coordconv.exam (This is a simple example which just converts the toxd.pdb file to different formats)