Calculations

CALC INTRA ((El1 r1 El2 r2 ..)/(TOLA p1)) (NOBOND) (NOANG)
(NOTOR) (NOLSPL) (NORING) (NOTMA) (NOBPA) (NOSTD) (WLSPL)
(NOPESD) (NOMOVE) (NOSYMM) (VERIFY) (TOLP t2)

The default instruction CALC INTRA produces a full calculation and listing of all relevant intra-molecular geometrical parameter options using default covalent radii drawn from internal tables. Atoms with distances less than the sum of their covalent radii plus a tolerance (TOLA = 0.4 Angstrom) are considered to be bonded. The default radii values may be modified with their explicit specification (in which case TOLA is set to zero, unless specified explicitly). Alternatively the parameter TOLA may be modified. In the automatic radii mode an additional 0.6 Angstrom is added to the tolerance to catch (Earth)alkali to non-metal contacts.

The calculation and listing of bonds, bond angles, torsion angles, least-squares planes, rings, angles between bonds and least-squares planes and thermal motion analysis may be suppressed with the specification of the sub-keywords NOBOND, NOANG, NOTOR, NOLSPL, NORING, NOBPA and/or NOTMA. The calculation of standard deviations may be suppressed with NOSTD.

The NOMOVE sub-keyword has the effect that atoms are left at their input positions in the course of the generation of a connected set.

The sub-keyword VERIFY may be used to control the inclusion of a connection in the bond list for plotting.

TOLP is an out-of-plane deviation parameter (by default 0.1 Angstrom) that determines the inclusion of an atom in the process of automatic least-squares plane search.

NOPESD , when specified, has the effect that the e.s.d. of the plane parameters is not included in the calculation of the e.s.d. in out-of-plane deviations.

WLSPL invokes mass-weighted least-squares plane calculations as opposed to unit weighted.

NOSYMM limits the search for connections within the input coordinate set without the application of translation or rotation symmetry.

        Example:
        CALC INTRA NOLSPL NORING  

CALC GEOM (SHELX/OMEGA/MOGLI/EUCLID) (VERIFY) (NOMOVE) (EXPAND)

This instruction executes a short intra calculation, mainly producing a list of bond distances, bond angles and torsion angles, as an alternative for the exhaustive CALC INTRA calculations. The sub-keyword SHELX may be used to generate an ordered coordinate file suitable for SHELX; OMEGA generates a file suitable for the tabulation of primary and derived parameters; MOGLI results in a DGE-file suitable for the program MOGLI and EUCLID gives a new SPF style file.

The NOMOVE sub-keyword has the effect that atoms are left at their input positions in the course of the generation of a connected set.

The EXPAND option may be useful for the generation of a file with the complete molecule as opposed to just the unique part.

        Example:
        CALC GEOM EUCLID EXPAND

CALC TMA

This invokes the execution of a rigid-body thermal motion analysis and the calculation of derived quantities. It is automatically included in a CALC INTRA calculation.

Note: No TMA analysis is done when the residue contains too few atoms or when the R-index of the observed and calculated Uij's is too high.

CALC INTER (El1 p1 El2 p2 ..)/(TOLR p1)

Short inter-molecular contacts are listed with this instruction. By default van der Waals radii drawn from internal tables are used in conjunction with a default tolerance (TOLR = 0.2 Angstrom). Hydrogen bonds are automatically found and analyzed.

CALC HBOND (p1 p2 p3)

This instruction provides a subset of the information generated with the CALC INTER instruction and may be of use when interest is concentrated on H-bonds.

CALC COORDN(p1/El1 r1 El2 r2 .. (NOANG) FIVE (TBA))

This instruction provides for the analysis of coordination spheres. Bond distances and bond angles are calculated for atoms within the specified sphere. By default such a calculation is done for all atoms (excluding C and H) and with radius 3.2 Angstrom. This default may be changed with the specification of the desired value. Alternatively a list of selected elements and their corresponding coordination radii may be specified for the coordination geometry calculations. Bond angles may be excluded from the listings with the NOANG sub-keyword. A Berry pseudo rotation analysis is carried out automatically when an atom is found to be bonded to exactly 5 atoms. Such a calculation may be enforced for the five shortest contacts with the sub-keyword FIVE optionally followed with the value for the trans-basal-angle (default 150 degree).

CALC COORDN atom_name p1

The coordination geometry about a single atom may be examined with this instruction.

        Example:
        CALC COORDN O3 3.2

CALC METAL (p1)

Distances between metal atoms less than p1 (default 10 Angstrom) are calculated. This option is included in the default CALC calculations.

CALC VOID (LIST) (GRID p1) (TOLV p2)

This option may be used to check the structure for voids as possible sites for solvents. The GRID (default value 0.4 Angstrom) and the minimum VOID radius (1.2 + p2 Angstrom) may be changed (default p2 = 0.0). The LIST option gives a map on the lineprinter. Positions with a shortest contact distance to the van der Waals surface of at least 1.2 + p2 Angstrom are indicated with >. Solvent accessible areas are indicated with a dot. Blank areas indicate small voids, all other gridpoints are within the molecular van der Waals volume.

Note: This option may also be used to study cases where the unit cell contents are misplaced with respect to the symmetry elements, since this fault will generally result in both areas with short molecular contacts and areas with voids.

The VOID option is more compute intensive than the rest of the instructions. It is advised to run this option in BATCH mode.

CALC DIST (eltype p1)

A distance scan is done for all vectors between the specified element and within the specified radius. By default a scan is done for H-atoms.

        Example:
        CALC DIST I 4.0

DIST Atom_name1 Atom_name2

With this option a distance between two specified and not necessarily bonded atoms may be calculated between atoms in the atom_array.

ANGL Atom_name1 Atom_name2 Atom_name3

The angle between the specified and not necessarily bonded atoms is calculated.

TORS Atom_name1 Atom_name2 Atom_name3 Atom_name4

The dihedral angle involving the four specified atoms (not necessarily bonded) is calculated.

LSPL Atom_name1 Atom_name2 Atom_name3 Atom_name4 ...

The least-squares plane determined by the specified atoms is calculated.