# ReadListPdb

NAME

    ReadPdb - read PDB file
    ReadOldPdb - read PDB file using old nomenclature
    ReadListPdb - read list of PDB files

SYNOPSIS

    ReadPdb fileName
    ReadListPdb fileName

DESCRIPTION

Read a PDB file. The file can contain more than one structure. If only one structure is stored in the file, the file name is taken as name of the molecule. If there are multiple structures, numbers are appended to the file name for generating the molecule names.

ReadListPdb expects a file with one file name per line (empty lines allowed), and reads all these files.

If residues appear in the residue library ($MOLMOLHOME/setup/amber94.lib by default, can be changed with the `PathNames` command), the covalent structure is taken from there. If a residue is not present in the library, just the atom coordianates are read from the PDB file. The user can add bonds with the command `CalcBond` later.

Because the PDB naming conventions (i.e. nomenclature changes) do not fully correspond with the names in the residue library of MOLMOL, a translation table for atom names is used by `ReadOldPdb`. This is $MOLMOLHOME/setup/PdbAtoms by default, and can be changed with the `PathNames` command.

The command also reads secondary structure information (HELIX and SHEET records) and sets the corresponding properties on the residues. They are used by the `AddRibbon` command to create schematic drawings.

EXAMPLE

    ReadPdb /home/joe/struct/my_prot.pdb
    ReadOldPdb /home/joe/struct/my_prot.pdb
    ReadListPdb /home/joe/struct/my_prot.nam

SEE ALSO

`PathNames`, `ReadAng`, `ReadDg`, `WritePdb`, `CalcBond`, `AddRibbon`

DATE

950704