Program Operation

The most common operations performed by Convert are to convert to and from PDB format, and to and from Frodo's DSN2 format. An example of each operation is given below.

Converting PDB to ATOMC format

$tntbin/convert << $eof
INCLUDE $tntdata/connect.dat
PDB pdb1tmn.ent
INCLUDE $tntdata/pdb_fixup.dat

PUNCH 1tmn.cor ATOMC
PUNCH 1tmn.seq SEQUENCE
$eof
if ($status >< 0) then exit 1

This example reads the PDB file named pdb1tmn.ent and produces the TNT coordinate file 1tmn.cor and the sequence file 1tmn.seq. If you do not need a sequence file simply delete the second PUNCH command. This example will work for any PDB file. Since the shell command from_pdb can be used to perform this conversion you do not need to write one of your own.

ATOMC to PDB format

$tntbin/convert << $eof
CELL 94.1 94.1 131.4 90 90 120
INCLUDE 1tmn.cor
INCLUDE 1tmn.seq

PUNCH 1tmn.pdb PDB
$eof
if ($status >< 0) then exit 1

This example writes the coordinates and sequence information stored in 1tmn.cor and 1tmn.seq to the PDB file 1tmn.pdb. The to_pdb shell command performs this function.

Converting DSN2 to ATOMC format

$tntbin/convert << $eof
INCLUDE $tntdata/connect.dat
DSN2 tln_phs5r.dsn2  15 P 17 CL- 30 ZN++ 20 CA++

PUNCH tln_phs5r.cor ATOMC
PUNCH tln_phs5r.seq SEQUENCE
$eof
if ($status >< 0) then exit 1

This example reads the DSN2 file named tln_phs5r.dsn2 and produces the TNT coordinate file tln_phs5r.cor and the sequence file tln_phs5r.seq. (The atom type translation table is unneeded if the DSN2 file was produced by Convert.) If you do not need a sequence file simply delete the second PUNCH command. This example will work for any DSN2 file. Since the shell command from_dsn2 can be used to perform this conversion you do not need to write one of your own unless you have special atom type codes.

Converting ATOMC to DSN2 format

$tntbin/convert << $eof
CELL 94.1 94.1 131.4 90 90 120
INCLUDE 1tmn.cor
INCLUDE 1tmn.seq

PUNCH 1tmn.dns2 DSN2  15 P 17 CL- 30 ZN++ 20 CA++
$eof
if ($status >< 0) then exit 1

This example writes the coordinates and sequence information stored in 1tmn.cor and 1tmn.seq to the DSN2 file 1tmn.dsn2. The shell command to_dsn2 performs this function.