The rrRNAv1 model is a reduced or simplified representation of RNA and associated proteins. The RNA is represented by one pseudoatom per nucleotide; this is located at the phosphorus atom and is called the P-atom. Helical regions are explicitly modeled by cross-linking the P-atoms that make up the stem and the interior of the helix is filled with another type of pseudoatom, called X-atoms. A network model is used for the proteins; a network of alpha carbon atoms. Thus, the rrRNAv1 model explicitly includes secondary structures. A description of the secondary structure and other information must be provided to the force field assembler. This tends to be complicated and is best defined in a Python module. The rrRNAv1 subpackage contains the descriptions (called blueprints) of several standard molecules. See the next chapter for how to prepare blueprints. The standard molecules are described in the STDMOL module. The force field consists of five terms: Bonds, Angles, Impropers, SoftSphereX. and ElectroX. The SoftSphereX term is used to provide bulk to the chain of P atoms in RNA and the alpha carbon atoms in proteins. Additionally, this term provides bulk to the interior of helical regions, via the X-atoms. The ElectroX term is designed to produce a proper charge list for the parmtop file but is normally switched off for Yammp calculations. Modules are located within the Yup package at Yup/Models/rrRNAv1/. The FFA, STDMOL and Analyzer modules are designed for public use while the other modules are not. Module Summary const Constants for the rrRNAv1 modules: constructor functions and labels for the force terms; the location of the parameter library and a table containing atom inclusion types, atom exclusion types, atomic masses and patterns. motifs Functions that take care of the details of the force field assembly of rrRNAv1 models. parmtop A link to the ParmTop module to convert the Yammp force field to the AMBER parmtop format. STDMOL Dictionary of predefined molecules. FFA Force Field Assembler Class and Function to create and manipulate rrRNAv1 models. Analyzer Functions to analyze rrRNAv1 models The const module defines the default parameter library as Yup/Data/rrRNAv1/ (within the Yup package). The user can create and use a different library. In order to do this, first create a text file called source-of-constants in a previously empty directory. See FPF for the format of this document or copy it from the standard parameter library. Do not change the number of, or the names of, the inclusion and exclusion atom types. You can only modify existing interaction types (change the force field parameters), add new interaction types, or remove existing interaction types. (An interaction type is a combination of atom types, for example, a pair of atom types form a Bonds interaction type. It is necessary to define interaction types for all combinations that can occur in a model. At the same time, it is desirable to omit interaction types for illogical combinations, e.g., for two atom types that cannot form a bond.) When source-of-constants is ready, run the program Yup.fpf to convert it to a number of database files. Pass the path (to the enclosing directory) to the constructor function FFA(). The force field assembler is subclassed from the template FFA in Yup.Tools.FFA. Initial coordinates can be crystallographic or generated using the randomline() routine in Yup.Tools.MakeLine. Preparing Molecular Descriptions Force Field Assembly Analysis Service Functions