Introduction The Emmental model represents a molecular system that is under the influence of a force field derived from a density map. The goal is to optimize the fit of the molecules into the density map.
The force field consists of two to four terms: Hooke and SwissCheeseX always, and Noens and SoftSphereX sometimes. The Hooke term is used to construct a Gaussian Network model of the molecule. The SwissCheeseX term represents the density map as a cloud of immobile points in space, and each point attracts the atoms in its neighborhood. The Noens term is used to construct an optional bubble to confine the molecular model to the density map. The SoftSphereX term is used to prevent atom overlap, which can occur if the Gaussian Network is not sufficiently stiff.	YUP.SCX INTRODUCTION TUTORIAL YUP.SCX YUP.VLAT EMMENTAL
Modules are located within the Yup package at Yup/Models/Emmental/. The Prepare, FFA, Calculate and Analyze modules are designed for public use while the other modules are not. Module Summary const Constants for the Emmental modules: labels for the force terms, inclusion and exclusion atom types and tables of interaction types. Prepare Functions to prepare data files required by this module FFA Force Field Assembler functions to create and modify Emmental models. Calculate Functions for the optimal placement of the molecular model in the density map. Analyze Functions to analyze Emmental models The const module defines the parameter library as Yup/Data/Emmental/ (within the Yup package). However, the user can create and use a different parameter 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 Hooke 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.) 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 NewModel(). To use the Emmental sub-package, start a Python interpreter and import each module. First, prepare the data files using the functions in Yup.Models.Emmental.Prepare. Then create an Emmental model using the functions in Yup.Models.Emmental.FFA, assigning the model object to a symbol. You can then use one of the fitting method in the Yup.Models.Emmental.Calculate module to achieve an optimal fitting of the molecule into the density map. Finally, use the functions in Yup.Models.Emmental.Analyze to examine your results and to write out the finished coordinates. Using this sub-package directly requires a knowledge of Python programming but you will have access to all the options. A command-line script, Yup.scx, is also available; it does not require any Python or programming skills but only a small number of the most widely used options are available. You can read the default parameters from Yup/Data/Emmental/source-of-constants and the source code for this sub-package is available at Yup/Models/Emmental/. The location of the root Yup/ varies from site to site. Type the command Yup.which to see where it is installed on your system. Data Preparation Force Field Assembly Calculate Analyze Utilities