Write saves the molecule model in model_number (not preceded by #) as a PDB file named filename. If filename is omitted, a dialog for specifying the name will appear. Only atomic coordinates and secondary structure records are saved; atomic display status, color, and radius are not included. The write command does not work for non-molecule models (surfaces, VRML models, etc.).
The relative option specifies that the coordinates written out are relative to the untransformed coordinates of model n; otherwise, the coordinates are written as currently transformed. Now that filename can contain spaces, the relative option can no longer be specified at the end of the line.
See also: pdbrun, save, write PDB in the Model Panel