Alpha face
The cross product of two bond vectors yields a directional vector, this is used to determine the alpha face direction. NAMOT2 uses this user provided information to orient the unit and bases after the diagonalization of the moment of inertia matrix. The N1-C2 and C2-N3 vectors are used to calculate the cross product. For purines a positive cross product is defined as Alpha face up, for pyrimidines a negative cross product is defined as Alpha face up.
The molecular modeling package AMBER produces an output that it refers to as "PDB" but differs from true PDB in several areas, enough so to warrant a separate set of handling routines.
NAMOT assigns its axes in accordance with the Cambridge convention.
Rotation of a base about the X axis.
The Corey-Pauling-Koltin model depicts each atom as sphere with a radius equal to its van der Waals radius.
Encapsulated PostScript(EPS)
Encapsulated PostScript is an extension of the PostScript language. EPS is designed to be incorporated into other PostScript documents. NAMOT2 produces EPS output, which is for all intents and purposes the same as PostScript.
a series of units with the same number of bases in each unit.
One of the two forms of specifiers in NAMOT2. It is
Helix #number:Unit number:Base number:Atom name
This can only be used to refer to molecules that have been loaded as a nucleic acid. The H:U:B format must be used to change the nucleic acid structure.
One of the two forms of specifiers in NAMOT2. It is
Molecule #number:Chain number:Group number:Atom name
This can be used to refer to any molecule loaded into NAMOT, but cannot be used to specify geometry changes.
A XWindow toolkit used mostly OSF/SYSV flavor unix workstations.
Nucleic Acid MOdeling Tool.
Rotation of a base about the Z axis.
The coordinate format of the Brookhaven Protein Databank.
A graphic file format that is easily converted to more popular formats (e.g., GIF & JPEG).
PostScript is a graphics language used predominately in printing applications.
Propeller twist
Rotation of a base about the Y axis.
Rotation of a unit about the Y axis.
Rotation of a unit about the X axis.
Rotation of a unit about the Z axis.
One or more bases designated as one entity. These are the modules that comprise helices.
Unit atom(UA)
A system in which the hydrogens are treated implicitly(i.e., a methyl group become one pseudo-atom with atomic mass 15)
A XWindow toolkit built on the OpenLook toolkit used mainly on Sun workstations, though is being replaced by Motif as Sun's supported windowing toolkit.