file extension MML

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes and on-line help. The display possibilities include conventional presentations, as well as novel schematic drawings, with the option of displaying different presentations in one view. The covalent molecular structures can be modified by addition or removal of individual atoms and bonds; the three-dimensional structure can be manipulated by interactive rotation about individual dihedral angles. Special efforts were made to allow for appropriate display and analysis of sets of (typically 20-40) conformers that are conventionally used to represent the result of a NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms.