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Unique Keywords for Specifying Data

CONVERT: Unique Keywords

DIAMOND <File name> N(<Atom type code>  <Atom type name>)

This statement allows the program to read the atomic coordinates from a Diamond format file. The file name of the Diamond file is the first item after the keyword. It is followed by a list of translation pairs. These pairs describe how the integer atom types of the Diamond file should map onto the atom type names that this package uses to identify atoms. The pairs (1 C), (2 N), (3 O), (4 S), and (5 P) are built into the program. If there are no other atom types in your structure and the above translation pairs are correct then you don't need to worry about atom type codes at all. Just give the file name and nothing else.

A CELL statement must precede a DIAMOND statement. If a sequence file is desired the file $tntdata/connect.dat must be INCLUDEd before this statement.

The coordinate system of the atoms in the Diamond file is assumed to be crystallographic Ångstroms (fractional times the cell edges). No other coordinate system of DIAMOND file can be read or written.

Here are some examples:

tabular891

The first example tells the program to read the file gewl.rdi and to use only the normal translation table. The second statement tells the program to read the file phase5r.rdi and to add another atom type to the translation table. The pair of values says that atom type 12 corresponds to the atom type MG++.


DSN2 <File name> N(<Atom type code> <Atom type name>)

This statement allows the program to read the atomic coordinates from a Frodo DSN2 format file. The file name of the DSN2 file is the first item after the keyword. It is followed by a list of translation pairs. These pairs describe how the integer atom types of the DSN2 file should map onto the atom type names that TNT uses. The pairs (1 C), (2 N), (3 O), (4 S), and (5 P) are built into the program. If there are no other atom types in your structure and the above translation pairs are correct then you don't need to worry about atom type codes. Just give the file name and nothing else.

If the DSN2 file was created by TNT the file will contain all the information required to translate the integer atom codes into TNT style atom type names. You do not need to enter any additional information.

If the DSN2 file does not contain cell constant information the DSN2 statement must be preceded by a CELL statement. If a sequence file is desired the file $tntdata/connect.dat must be INCLUDEd before this statement.

Here are some examples:

tabular901

The first example tells the program to read the file gewl.dsn2 and to use only the normal translation table. The second line tells the program to read the file phase5r.dsn2 and to add an additional atom type. The entry says that atom type 12 corresponds to the atom type MG++.


HENDRICKSON <File name>

This statement causes the program to read the named file into the internal data base. This allows the input of Hendrickson format coordinates. A CELL statement is required in all cases and $tntdata/connect.dat should be INCLUDEd if a sequence file is desired. The name of the atom type of each atom is assumed to be the first character of the atom name. If there are atoms in the structure whose type cannot be determined by this method you will either have to use the RENAME command in your script or edit the file.


PDB <File name>

This statement causes the program to read the named file into the internal data base. This allows the input of Protein Data Bank format coordinates. Cell constant information is read from the file so a CELL statement not is required. The file $tntdata/connect.dat must be INCLUDEd before the PDB statement if a sequence file is desired. The elemental type of each atom is determined from the first two columns of the atom name field. While this method usually gives the correct elemental type it cannot give the ionic state of the atom. This information will have to be given either using the RENAME command or manually editing the final coordinate file.

While $tntdata/connect.dat should be INCLUDEd prior to the PDB statement it is usually wise to INCLUDE the file $tntdata/pdb_fixup.dat afterwards. This file will correct a wide range of possible problems, including the correction of most elemental types.

Convert will automatically change the C-termini from PDB style to TNT style. It will move the extra oxygen atom into a residue of its own and link it with a CTERM linkage. Convert will also read the disulfides off the SSBRIDGE statements and include then in the new sequence file.

Convert will not properly create a sequence file for DNA or RNA, although it will be close. See Page gif for details.


next up previous contents index
Next: Command Statements Up: CONVERT Previous: Keywords for Inferring the

Dale Edwin Tronrud
Thu Jul 6 23:24:57 PDT 2000