DISTANG (CCP4: Supported Program)
NAME
distang
- Distances and angles calculation
SYNOPSIS
distang xyzin
foo_in.brk
[Keyworded input]
DESCRIPTION
DISTANG is a general purpose program for calculating atomic
distances within a protein molecule, and between symmetry
equivalent molecules within a crystal lattice.
It is based on Sam Motherwell's program DJANGO,
developed for the Cambridge Data Base (and that goes back to John
Rollett's original algorithm!).
PROGRAM FUNCTION
The functions of the program DISTANG may be summarised as follows:
-
To calculate bond distances for a subset of the coordinates
stored in a Brookhaven format file.
-
To calculate bond angles for a subset of the coordinates
stored in a Brookhaven format file.
-
To calculate possible packing restrictions for a coordinate set.
-
To generate information in a suitable format for the PROTIN
dictionary from a set of coordinates stored in Brookhaven format.
The standard options are driven by the keyword DISTANCE using
combinations of the subsidiary keywords ALL or VDW and INTER or INTRA.
Another useful option is to do a packing search. If the
orientation of a molecule is known, various translational
parameters can be tested to find those which give impossible
packing.
See GRID for details about this.
KEYWORDED INPUT
All control input is in free format with keywords specifying the
options required. The possibilities are:
ADDRADIUS, ANGLE, DISTANCE,
DMIN, END,
FROM, GRID,
LIST, OUTPUT,
RADII, SYMMETRY,
TITLE, TO, TORSION
The only compulsory one is RADII.
DISTANCE [ VDW | ALL ] [ INTER | INTRA ]
- VDW
-
(Default. ) Only contacts between atoms not in the same, or adjoining,
residues are printed.
- ALL
-
all contacts to be output, even those within one residue.
- INTER
-
Calculate intermolecular distances.
- INTRA
-
(Default.) Calculate intramolecular distances.
If SYMMETRY is specified INTRA will include INTERmolecular contacts too.
SYMMETRY <SG>
Followed by a spacegroup name or number or explicit symmetry operator
in the standard form.
RADII <atomid> <radii> ...
[COMPULSORY INPUT]
Set search radii for atom types.
A list of atom types and radii follows on the
same line.
Default values are: CA 1.5 C 1.5 N 1.5 O 1.5 SG 1.5 OW 1.5
e.g.: RADII CA 2.2 OW 1.5 ZN 2.0 C 1.7 N 1.7 O 1.7
The program tries to match the atom name to
the 2 character atom types first, and if none
are found to the 1 character atom types.
This allows you to set different radii for CA
and other Carbon atoms say, but there is an
unsolved problem for CAlcium.
If the atom name does not match it is ignored
(Beware lost SG etc.)
FROM [ [ ATOM <inat0> [TO] <inat1> ] | [ RESIDUE <ires0> [TO] <ires1> ]] ... [ CHAIN ALL | ONS | CA ]
TO [ [ ATOM <jnat0> [TO] <jnat1> ] | [ RESIDUE <jres0> [TO] <jres1> ]] ... [ CHAIN ALL | ONS | CA ]
Sets atom limits. (Default all atoms to all.)
If ATOM is specified it is followed by <inat0> and <inat1>,
respectively the first and last target atoms checked. I.e. FROM
atoms <inat0> to <inat1> are checked against TO atoms <jnat0> to <jnat1>.
(Atoms are numbered 1 to NAT, in the order read, but the residue order
can be varied without restriction. Beware: atoms with occ=0.0 are
not counted.)
If RESIDUE is specified it is followed by <jres0> and <jres1>,
respectively the first and last target residues checked,
and optionally subsidiary keywords:
- CHAIN ALL | ONS | CA
-
ALL (default) will select
all atoms in the requested residues. ONs will select just the oxygen
and nitrogen atoms. CA will select just the CA atoms.
-
i.e. FROM residues <ires0> to <ires1> (CHAIN <type>) are checked against
TO residues <jres0> to <jres1> for the appropriate class of atoms.
ANGLE
Calculate bond angles between bonded atom triples.
ADDRADIUS <addrii>
Value added to the value given by the RADIUS keyword.
Only applies if the RADIUS keyword is also given.
DMIN <dmin>
The minimum distance printed is dmin
LIST <natoms>
List fractional and orthogonal coordinates for first <natoms> atoms.
OUTPUT [ LPOUT | KHCONN | PDBCONN ]
- LPOUT
-
list distang output to a file assigned to PRJOUT.
- KHCONN
-
list pseudo-PROTIN distance dictionary output to
a file assigned to KHCONN. Only 250 atoms are allowed for this option.
(See RWDICT to prepare residue type entry for dictionary.)
- PDBCONN
-
list PDB type file containing CONECT lines to a
file assigned to PDBCONN.
Only 250 atoms allowed for this option.
GRID <xmin> <xmax> <dtx> <ymin> <ymax> <dty> <zmin> <zmax> <dtz>
All in fractions of unit cell.
Define search grid for a correctly oriented molecule through
asymmetric unit. The coordinates are translated over the grid and a
table of the number of bad contacts is generated; i.e. it is a sort of
packing search. It sets all RADII except that for CA equal 0 to save
time. The default RADII for CA is 2.0Å but you can reset this.
TITLE <title>
Title to print on output.
TORSION
Calculate torsion angles between bonded atom
quadruples. Probably will not work but there
is residual code for any eager programmer to
look at.
END
triggers calculation.
NOTES
-
Size limitation: a maximum of 40000 atoms is handled.
-
It is ESSENTIAL to give CRYSTAL and SCALE lines in the input
coordinate file. These are needed for generating symmetry
equivalents.
EXAMPLES
distang XYZIN $CTEST/toxd/toxd.pdb << END-distang
SYMM 19
dist vdw INTRA
RADI C 1.5 CA 1.5 N 1.5 O 1.5 OW 1.6
FROM ATOM 1 TO 1000
TO ATOM 1 to 200000
END
END-distang
distang XYZIN $CTEST/toxd/toxd.pdb << END-distang
SYMM 19
dist vdw INTRA
RADI C 1.5 CA 1.5 N 1.5 O 1.5 OW 1.6
FROM RES ALL CHAIN A 1 to 125
TO RES ALL CHAIN W 1 to 256
END
END-distang
# Calculate distance angles for B2 c-unique contacts.
#
distang XYZIN $CTEST/toxd/toxd.pdb << END-distang
SYMM P212121
dist all
angle
RADI C 0.8 N 1.5 O 1.5 OW 1.6
FROM ATOM 1 TO 561
TO ATOM 1 TO 561
END
END-distang
# Calculate distance angles and output PROTIN type distance list.
# for a new substrate (Prepare other parts of dictionary with RWDICT)
distang KHCONN $CCP4_SCR/junk.kh XYZIN substrate.pdb << END-distang
SYMM 19
output khconn
dist all
angle
RADI C 0.8 N 0.8 O 0.8 P 1.3
FROM ATOM 1320 TO 1350 ! Atoms in a substrate perhaps.
TO ATOM 1320 to 1350
END
END-distang
# A grid search: check your rotation function
distang XYZIN taka_2065115.pdb << EOF
SYMM 170
DIST VDW INTER
RADI CA 1.8
GRID 0 1 0.05 0 1 0.05 0 0 1
FROM ATOM 1 TO 10000
TO ATOM 1 TO 10000
END
EOF
SEE ALSO
Alternative contact analysis:
REFERENCES
-
IUPAC-IUB conventions, J. Mol. Biol., 50, 1 (1972).