Molecular Structures in NMRView

The best way to read a molecular structure into NMRView is to first read a sequence file in NMRView format (the same as that used by PEGASUS). A sequence file consists of a line for each residue, each line containing the three-letter code for the amino-acid. NMRView will try to find a corresponding residue in its residue library, (in the directory $NMRVIEWHOME/reslib) and read in the molecular topology. To read a sequence use the nv_sread seq command or select Read AA Sequence from the Molecules menu on the main NMRView control panel. The topology will be stored in the current database, and need not be read in again during future NMRView sessions. To read in molecular coordinates (after having read the topology) use the nv_sread xyz command to read xyz coordinates from files in the Brookhaven Protein Data Bank (PDB) format. The file will be scanned and coordinates of atoms whose name and residue number match an atom in the internal topolgy will be read in. These coordinates will also be stored in the current database, and need not be read in again during future NMRView sessions. Up to 100 structures can be read and stored in separate memory locations.