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!). It will be almost completely superseded by Eugene Krissenel's new ncont program, but there are still some functions which are useful.

PROGRAM FUNCTION

The functions of the program DISTANG may be summarised as follows:
  1. To calculate bond distances for a subset of the coordinates stored in a Brookhaven format file. The atomic radii can be chosen by the user. This is very useful when examining the distribution of heavy atoms or anomalous scatterers and checking for non-crystallographic symmetry.
  2. To calculate bond angles for a subset of the coordinates stored in a Brookhaven format file.
  3. To calculate possible packing restrictions for a coordinate set.
  4. To generate information in a suitable format for WATERTIDY from a set of coordinates stored in Brookhaven format.
    Important: post CCP4 V4.2, WATERTIDY cannot read the logfile from DISTANG directly. Instead the OUTPUT DISTOUT option of DISTANG must be used - the resulting output file assigned to DISTOUT will be in the appropriate format to be read in by WATERTIDY.
  5. To generate information in a suitable format for the PROTIN dictionary from a set of coordinates stored in Brookhaven format.

The type of distances listed is controlled 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

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
Lists intermolecular distances only.
INTRA
(Default.) Calculates intra and inter-molecular distances.

SYMMETRY <SG>

Followed by a spacegroup name or number or explicit symmetry operator in the standard form. If the Spacegroup is given in the coordinate header this is used by default.

RADII <atomid> <radii> ...


Resets search radii for different 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 S 1.5 OW 1.5 P 1.5 SE 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. All atom types are upper case.

If the atom name does not match it is ignored

FROM ATOM <inat0> [TO] <inat1>

FROM RESIDUE <ires0> [TO] <ires1> [ CHAIN <chainID> ] [ ALL | ONS | CA ]

TO ATOM <jnat0> [TO] <jnat1>

TO RESIDUE <jres0> [TO] <jres1> [ CHAIN <chainID> ] [ 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 <chainID>
Chain ID for the specified residue range.
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> 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 [ LINKS | LPOUT | DISTOUT | KHCONN | PDBCONN ]

LINKS/LPOUT
writes the coordinate pairs for each link to a file assigned to XYZOUT. (These keywords are synonyms for each other.)
DISTOUT
The "old-style" DISTANG output is written to a file assigned to DISTOUT. This is required for the program WATERTIDY.
KHCONN
list pseudo-PROTIN distance dictionary output to a file assigned to KHCONN. Only 250 atoms are allowed for this option. (See MAKEDICT 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

  1. Size limitation: a maximum of 60000 atoms is handled.
  2. It is ESSENTIAL to give CRYSTAL and SCALE lines in the input coordinate file. These are needed for generating symmetry equivalents. If the spacegroup is given the SYMM keyword is not required.

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 symmetry contacts.
#
distang XYZIN $CTEST/toxd/toxd.pdb << END-distang 
SYMM P212121
dist inter 
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

#   Search a set of coordinate fragments to see if any should be linked
#  Useful after Arp/Warp scripts
distang XYZIN taka_2065115.pdb << EOF
SYMM 170
DIST VDW 
RADI  CA 3.8
FROM ATOM 1 TO 10000
TO ATOM 1 TO 10000
END
EOF  


# Search to se which SE might be associated with which molecule.
distang XYZIN chmi_s1.pdb XYZOUT chmi_s1-contacts.cds << EOF
outp link
symmetry P41212
radii  SE 10.0
end
EOF

#   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  


#   Output list of contacts in form suitable for WATERTIDY
distang DISTOUT $CCP4_SCR/distang.list XYZIN $CEXAM/toxd/toxd.pdb << END-distang 
SYMM 19
output distout
dist vdw 
#  Use default radii and search from protein atoms to solvent atoms
from atom 1 to 502
to atom 503 to 600
END  
END-distang

#   Output distance pairs to XYZOUT.
distang XYZOUT $CCP4_SCR/links.coords XYZIN $CEXAM/toxd/toxd.pdb << END-distang 
SYMM 19
output link
dist vdw 
#  Use default radii and search all atoms
END  
END-distang

#   Calculate distance angles  and output PROTIN type distance list.
#  for a new substrate (Prepare other parts of dictionary with MAKEDICT)
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

SEE ALSO

Alternative contact analysis:

REFERENCES

  1. IUPAC-IUB conventions, J. Mol. Biol., 50, 1 (1972).