When no UNIT number or file is specified, the READ UNIT is the current input, either the terminal or a command file. The number of atoms is changed only when cartesian or internal coordinates are read. The FILES are opened with the READONLY option.
READ UNIT int
FILE string
ATOMS DEFAULT ATOM_UNI INITIALIZE
CARD [ANGSTROEM] APPEND
PDB NANOMETER OVER SELECT ... END
XPLOR
DISCOVER
AMPAC
GROMOS
DIAMOND
SCATTERI
ELEMENTS
BONDS () | INITIALIZE
NUMBERS | APPEND
CTABLE | FIRST atom-num
HBONDS | SELECT ... END
ZTABLE |
INTERNAL (GAUSS) ATOM INITIALIZE
AMPAC (ANGSTROEM) (APPEND)
OVERWRITE FIRST *
POINTS ()
SURFACE CONNOLLY INITIALIZE
VOLUME GAUSSIAN86 (APPEND)
POTENTIAL G80 FIRST *
DENSITY
TOPOLOGY CARD (APPEND)
XPLOR INITIALIZE
DISCOVER
GROMOS
(MAIN)
PARAMETERS XPLOR
SEQUENCE
CELL
SYMMETRY
MAP (CHARACTER) OVERWRITE int
NUMBER
ALPHA
PROTEIN
XPLOR
CCP4
See READ ATOMS.
... ATOMS ATOM INITIALIZE
CARD APPEND
PDB NANOMETER OVER SELECT ... END
XPLOR
DISCOVER
AMPAC
GROMOS
DIAMOND
ATOMIC coordinates can be read in different formats. The program uses angstroems units. INITIALIZE starts reading from zero number of atoms. APPEND adds the atoms to the previously known ones in the program. OVERWRITE finds the FIRST atom number in the SELECTION and replaces the atomic coordinates after the first found atom and leaves the atom and residue structures untouched.
Formats: DEFAULT, CARD, PDB, XPLOR, DISCOVER, AMPAC, GROMOS, DIAMOND
The format without a name is the DEFAULT format. It tries to find an atomic name or atomic element number and 3 coordinates for X, Y, and Z. The format is free and the order of data is not important. When a real number is not found, the program assumes that the coordinate is zero.
CARD is the CHARMM format.
DIAMOND is the format used by FRODO and EREF.
PDB or XPLOR reads Brookhaven Data Bank and XPLOR PDB.
DISCOVER is the format from BIOSYM Inc. (DISCOVER, INSIGHT).
GROMOS is the Groningen package format.
AMPAC and GAUSSIANnn are program packages for quantum mechanical calculations.
Units:
ANGSTROEM units are the default.
NANOMETER accepts that the coordinates in NANOMETERS and multiplies them by 10. In GROMOS format the NANOMETER units are set automatically.
ATOM means that coordinates have to be converted from atomic units to Angstroems. Atom units are quite often used in quantum mechanical calculations.
SCATTERING factors for each ELEMENT can be read in form of an ELEMENT id (and also as atomic number) followed by 10 or less real numbers (the 5 gaussian presentation as appearing in the International tables.)
Each atom has its ATOMIC NUMBER and ELEMENT id. When read each atom gets its ATOMIC NUMBER based on comparison with the ELEMENT id-s table. Each ELEMENT id, which is a string, can be replaced by reading a line consisting of an ATOMIC NUMBER and the new ELEMENT id string. Replacing C with E for example:
>read element > 6 E >
If a new name is not unique, then it can not replace the old one. All characters are converted to capital letters. See also WRITE ELEMENTS.
... BONDS NUMBER
A file containing only the atom numbers is read when there is the NUMBER command word.
... CTABLE
A connection table can be read. This make sense only when atoms are in the same order as they were when the CTABLE was written.
... ZTABLE
A Z-mat-connection table is used for conversions between the INTERNAL (relative) and cartesian COORDINATES (absolute). Each atom can have a ZTABLE record.
... INTERNAL GAUSSIAN
AMPAC
Reads INTERNAL coordinates and ZTABLE with the INITIALIZE or APPEND options. GAUSSIAN or AMPAC formats can be read.
... POINTS ()
SURFACE CONNOLLY INITIALIZE
VOLUME GAUSSIAN86 (APPEND)
POTENTIAL G80 FIRST *
DENSITY
SURFACE, VOLUME, electrostatic POTENTIAL or DENSITY POINTS can be READ. The default is SURFACE points. When the read points are to be transformed into some other kind (VOLUME, electrostatic POTENTIAL or DENSITY) then the kind should be explicitly specified.
There are three formats of point records available (CONNOLLY, GAUSSIAN86 and G80). Only the CONNOLLY format includes the complete information for each point. The GAUSSIAN86 and G80 formats are only used to READ electrostatic potentials.
The POINT counter can be set to 0 (INITIALIZE) or left unchanged (APPEND). Each point has one or more atomic indices that tell the program to which atom a point belongs. By default they are not changed when using the CONNOLLY format. With GAUSSIAN and G80 all the points in the file are by default assigned to the last atom. The default can be changed by the FIRST option, so that the number of the first atom found in the SELECTION is supposed to be the atomic index 1 from the points. This is achieved simply by adding the difference to each atomic index.
... TOPOLOGY MAIN
CARD (APPEND)
XPLOR INITIALIZE
DISCOVER
GROMOS
MAIN format is the default. MAIN topology libaries are the only ones that can be used for model building and energy calculations.
The X-PLOR (XPLOR) TOPOLOGY files can used for energy minimization procedure, however, new residues can not be built from scratch from X-PLOR topology files. The conversion to MAIN topology files is rather simple, so that you should in general try to convert your XPLOR topology files in MAIN format.
The DISCOVER topology file of MOLEDT - DISCOVER format can be used can be used for model building (CLASSES, CHARGES, BONDS and INTERNALS are read).
The GROMOS and CARD (CHARMM) topology files can be used for atom name corrections and partial atomic charges assigneent (only CLASSES and CHARGES are read).
... CELL
Cell constants (a, b, c, alpha, beta, gamma) are read in free format. Title line(s) beginning with a '*' is required, when you try to read the cell constants from your terminal.
... SYMMETRY
SYMMETRY operations are read in the form used by the international tables for crystallography. Only a single group of crystallographic symmetry operations can be handeled at once in the program. When MAP files in PROTEIN or MAIN formats are read the symmetry operations are included automatically.
... MAPS CHARACTER OVERWRITE int
REAL (NUMBER)
ALPHA
CCP4
PROTEIN
XPLOR
Maps can be read by MAIN as character*1 or real*4 maps. The default map format is the CHARACTER. The real*4 maps require the NUMBER format qualifier. PROTEIN, XPLOR and ASCII CCP4 maps are transformed into the real*4 maps. ALPHA maps are a character*1 presentation written hexadecimally. ALPHA, XPLOR and ASCII CCP4 maps are all text files that can be transferred between any hardware.
ASCII CCP4 maps are output from a CCP4 program called mapexchange.
PROTEIN maps are automatically scaled to 1 sigma.
The OVERWRITE qualifier means, that the map stored under the specified map number will be overwritten and that all maps with higher consecutive numbers are lost.
... FIRST atom-num
SELECT ... END
The FIRST atom can be specified directly as an atom number or found as the first atom in the SELECTION.
... REFLECTIONS INITIALIZE
RESOLUTION real real
LIMITS int int int
FRIEDEL
RE_READ
MAIN
XPLOR
CSN
When INITIALIZING the data arrays RESOLUTION limits have to be specified and cell constants known to the program.
Reads a reflections file (with INDEX, FOBS, PHASE, SIGMA, FCALC, COMPLEX, POLAR, WEIGHT, TEST). FOBS can have PHASE too. FCALCs can be presented as COMPLEX numbers or as POLAR (amplitude and phase). Format is free.
The lower HKL limits are desired, in order to reduce data storage. If you don't know what to do set the LIMITS to zeros and use keyword RE_READ to get the exact values. RE_READ will read the reflection file twice in the case of a limits problem. It however makes sense that for future readings the limits are correctly set in order to avoid the unneccessary, time consuming second pass through a reflecion file.
TEST keyword flags are stored in the reflection KEY 'TEST' which can be used later on for R-FREE calculations.
Program interprets an XPLOR reflection file as well.
Specifies the CSN format. The follwoing keywords are processed INDEX, FOBS, SIGMA, IOBS, ISIGMA, FOM, PA, PB, PC, PD, however, only INDEX, FOBS, SIGMA and FOM are understood.