The WRITE sentence is used to write data to files or to the terminal. First the FILE or FORTRAN logical UNIT should be specified, then the SELECTION and after that the write object specification (COORDINATES, BONDS, INTERNAL, MAP), format (PDB, DIAMOND ...) and units (ANGSTROM, ATOMIC, NANOMETERS). The FILE, UNIT and SELECT are optional. When the FILE or UNIT are omitted the output comes to the terminal (SYS$OUTOUT). The default SELECTION are all atoms and the default length UNIT is ANGSTROM.
WRITE UNIT int
FILE string
OVER
APPEND
SELECT ... END
ATOM
NANOMETER
NUMBER (inte)
NAMES
COORDINATES NORMAL
CARD
PDB SEGMENT
XPLOR
DIAMOND
DISCOVER
GROMOS
GAUSSIAN
BOND []
NUMBER
CTABLE []
NUMBER
NAMES
FIRST SELECT ... END
HBOND
PAIR []
NUMBER
RAMACHANDRAN
ZTABLE
INTERNAL (GAUSSIAN) VARIABLES
AMPAC
POINT SURFACE ALL (CONNOLY)
REENTRANT GAUSSIAN
ACCESSIBLE G80
VOLUME ALL
ATOM
ACCESSIBLE
POTENTIAL
DENSITY
MAP inte NUMBER
CHARACTER
ALPHA
FFT
XPLOR
SYMMETRY
CELL
WRITE UNIT inte ...
WRITES the selected data to the FORTRAN logical UNIT number inte.
WRITE FILE string ...
WRITES the selected data to the FILE string.
... APPEND
Using APPEND it is possible to APPEND information to the end of an already existing file.
... OVER
Using OVER it is possible to overwrite an already existing file.
... SELECT ... END
When data related to atoms are WRITTEN a SELECTION can be applied. The SELECT ... END sentence should proceed the command word that specifies the kind of data. The default SELECTION are all atoms.
... []
ATOMIC
NANOMETER
The default length units are Angstroems. When COORDINATES are to be written in NANOMETERS and ATOM units, then the units should be explicitly specified.
... NUMBER (inte)
The NUMBER flag is the opposite of the NAMES flag. In common it means that the data are less descriptive and that NAMES are replaced by NUMBERS. In any case, the NAMES or NUMBER specifier must follow the write object specification. The meaning of NUMBER or NAMES has different meanings:
by COORDINATES:
by BONDS, PAIRS:
This is actually a format to write only the bond list containing only the atomic NUMBERS.
by CTABLE, ZTABLE:
Writes atomic NUMBERS of the reference atoms.
by MAP:
It is the real*4 MAIN MAP format.
... NAMES
The NAMES flag, is the opposite of the NUMBER flag and has a bit ambiguous meaning. In common it means that the description is more complete and that NUMBERS are replaced by NAMES. In any case, the NAMES or NUMBER specifier must follow the write object specification.
by COORDINATES:
by BONDS, PAIRS: This is the default form.
by CTABLE, ZTABLE: Writes atomic numbers of the reference atoms.
by MAP: It is the real*4 MAIN MAP format.
See WRITE ATOMS.
... ATOMS PLAIN
CARD
PDB REORDER
XPLOR
DIAMOND
DISCOVER
GROMOS
GAUSSIAN
ATOM
NANOMETER
NUMBER inte
NAMES
The length units applied are Angstroems (default for all formats except for GROMOS, where nanometers are used), NANOMETERS and ATOM units. The following formats are available: NORMAL, CARD, PDB, XPLOR, DIAMOND, DISCOVER, GROMOS, GAUSSIAN. The NUMBER and NAMES flag effect only PDB and XPLOR format. The ATOM and NANOMETER units could be applied anywhere.
The REORDER keyword is applied only with the PDB format. It reorders residues accoridng to their connectivities.
Write SCATTERING factors tells you which atomic numbers have their scattering factors defined and what are their Gaussian coeficient values.
Writes ATOMIC NUMBERS with ELEMENT IDS. The rule, what is written can be also READ is obeyed.
... INTERNAL (GAUSSIAN) VARIABLES
AMPAC
INTERNAL coordinates can be written with VARIABLE names and values too. VARIABLES are used by GAUSSIAN geometry optimization. The default format is the GAUSSIAN.
... ZTABLE
WRITES the ZTABLE list either with atomic NUMBERS or names (NAMES).
... BOND []
NUMBER
WRITES the BOND list. The default format is NAMES. The outout contains atom, residue, sequence and segment name of each atom included in the covalent bond and its length. When NUMBER is specified, then the BOND list contains only atomic numbers.
WRITE CTABLE NAMES
NUMBER
FIRST SELECT ... END
WRITES the connectivity table. The CTABLE contains the complete set of each atom names (atom, residue, sequence and segment NAMES) and its neighbours.
... NAMES
The neighbors are written with their atom NUMBER or atom NAMES. Atoms names are useful for debugging purposes only, they can, however, give you a better idea, which are the neighbours of a particular atom. The NAMES file can not be read again though.
... SELECT ... END
FIRST command enables you to modify the atom number when it is written to file. This way you can save connectivity tables of various molecules and later read them in a different order, again using FIRST command in a READ CTABLE sentence.
WRITE HBOND
WRITES the hydrogen bond (HBOND) list. The list contains the atom, residue, sequence and segment name of each atom included in the hydrogen bond list, its length and angle. Angle is written only when hydrogen atoms are present.
WRITE PAIR NAMES
NUMBER
RAMACHANDRAN
WRITES the PAIR list. NAMES is the default format. The outout contains atom, residue, sequence and segment name of both PAIRED atoms, the interatomic distance and when the equilibrium distance and force constant are DEFINED also these. With the NUMBER format only atomic NUMBERS are written.
When the PAIR list is defined as the RAMACHANDARN PAIR list then the PHI and PSI angles for each residue are written.
... POINT SURFACE ALL (CONNOLY)
REENTRANT GAUSSIAN
ACCESSIBLE G80
VOLUME ALL
ATOM
ACCESSIBLE
POTENTIAL
DENSITY
Points can be chosen according to their kind (SURFACE, VOLUME, DENSITY, POTENTIAL) written in 3 different formats (CONNOLY, GAUSSIAN86, G80). SURFACE and VOLUME points can be also further divided into (REENTRANT, ACCESSIBLE and ATOM, ACCESSIBLE) GAUSSIAN and G80 formats only write point coordinates. G80 is in atom units. So that appropriate programs can read them. Units and NAMES/NUMBER flag have no effect. The CONNOLY format is in Angstroems and the G80 format is in ATOM units.
WRITE MAP inte NUMBER
CHARACTER
ALPHA
FFT
XPLOR
The 'inte' tells which MAP to write and is required. When no format is specified the character*1 maps are written with the CHARACTER format and the real*4 maps with the NUMBER format. MAP can be written in 5 different formats (NUMBER, CHARACTER, ALPHA, FFT and XPLOR). The NUMBER, CHARACTER and ALPHA are MAIN formats, while the FFT format is unformatted and is the input for the FFT calculation using P1SF (Lyn Ten Eyck program) or PROTEIN and the XPLOR map is a formatted text file.
... SYMMETRY
WRITES the crystal SYMMETRY operations (matrices and translation vector).
... CELL
WRITES the crystal CELL constants.
MAIN> write unit 3 select atom name CA end coordinates pdb
MAIN> write file int_coor.dat internal variable - MAIN> first select number residue 2 end
MAIN> write select pro end point surface accessible
MAIN> write file cell.fft map 2 fft