nv_sread

Reads in one or more files, the type of which is specified by the option.

nv_sread pdb fileName

Read Protein Data Bank format files. This is the standard way to read in pdb files. NMRView first reads the pdb file to determine the amino acid sequence. Next, it reads the corresponding residues from the PEGASUS residue library. Finally, it reads coordinates from the pdb file for those atoms that have names matching the names in the residue library. Atoms, that do not have a match in the residue library will not be entered into the PEGASUS structure list. Atoms that are in the residue library but not in pdb file, will be included in structure list but will not be displayed. The file will be read from directory $SDIR where SDIR is a TCL variable. SDIR can be set in the preference panel or on the command line. The default value for SDIR is ".".

nv_sread grp fileName

Reads in coordinates from a series of PDB files. The first file is "filename0", second file is "filename1" etc. The command continues to read files until a file is unsuccesfully read or the maximum of 100 files have been read in. Each coordinate set is stored in successive structures. The command only reads in the coordinates. The commands "sread -seq", "sread -xpsf" or "sread -pdb" must have been used previously with a file with the same atoms. The directory used is the same as that used with "nv_read pdb" command.

nv_sread pdbs fileName

Read protein data bank files. Reads a file of atomic coordinates of a macromolecule. File must be stored in the PDB format as defined by Brookhaven National Laboratorie Protein Data Bank. This command does not also read from the PEGASUS residue library so no connectivity information is available. If this is needed use the pdb command instead. The directory used is the same as that used with "nv_sread pdb" command.

nv_sread xpsf fileName

Reads a file in the format produced by XPLOR. This is a alternative method to the sread -seq command to obtain atom, residue and connectivity information. Coordinates must be read in with the "sread -xyz" or "sread -grp" commands. The directory used is the same as that used with "sread -pdb" command.

nv_sread xyz fileName strct

Reads the PDB file filename and attempts to match the atoms to atoms in the structure in memory. If atoms match by residue name, atom name, sequence number, chain id, and alternate identifier then the coordinates corresponding to each atom matched are assigned the value of the coordinates of that atom in file. The coordinates are read into the structure specified by the "strct" parameter. The directory used is the same as that used with "sread -pdb" command.

nv_sread seq seqName

Read in residues from residue library based on sequence in file filename.