ReadPdb - read PDB file ReadListPdb - read list of PDB filesSYNOPSIS
ReadPdb fileName ReadListPdb fileNameDESCRIPTION
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 do not fully correspond with the names in the residue library of MOLMOL, a translation table for atom names is used. 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 ReadListPdb /home/joe/struct/my_prot.namSEE ALSO
PathNames, ReadAng, ReadDg, WritePdb, CalcBond, AddRibbon
DATE
950704