Introduction Data Preparation Force Field Assembly Calculate Analyze The Yup.Models.Emmental.Analyze module provides a number of functions to examine an Emmental model. ShowHooke, ShowSCX, ShowNoe, SCXScore The following functions take one argument, the Model object (created by the Yup.Models.Emmental.FFA module) and prints the results to the standard output. The output can be voluminous and is formatted for processing in a spreadsheet program. Function Print Output ShowHooke Six columns per pair of all the bonds in the Hooke term(s). ShowSCX Seven columns for each atom-hole pair that is currently within the cutoff distance in all the SwissCheeseX term(s). ShowNOE Eight columns per atom pair of the Noens term. SCXScore The total SCX energy, divided by the number of atoms, normalized by the depth of the deepest hole. Dimensionless, positive value, maximum value of 1 in most cases. SizeOfHooke, CenterOfMass The following functions take one argument, the Emmental Model object and return the value(s) to the caller. Function Type Return value(s) SizeOfHooke Integer The total number of bond pairs in the Hooke term(s). CenterOfMass Tuple of floats The center of mass (atomic weight is obtained for each atom after determining its element; all data come from the Yup.Tools.ChemNames module). PDBSCXScore This function takes two or three arguments, and will report the SCX score for a PDB file when it is placed on the named density map. Argument Type Preset Value Description pdbfile string the name of a PDB file scxfile string the name of a SCX-format density map file partmapfile string "XXX" Prefix for a temporary Partition Map file, which will be removed when the function exits. Best to use only letters of the alphabet. The Partition Map file has to be generated in order to calculate the SCX score. The file will be given a name with the specified prefix followed by nine digits generated at random. You must not have files with this naming scheme in the current directory or you will risk losing them. You may be able to avoid a name clash by changing the prefix. WritePDB The WritePDB() function takes one to five arguments and it will generate a PDB file for the given Emmental Model object. Argument Type Preset Value Description model Model The Model object for an Emmental model prefix string "SCX" leading part of the name of the output PDB file suffix string ".pdb" extension of the output PDB file verbose integer: 0 or not 0 1 whether to work silently or not shift None or list of floats None translate the coordinate before writing the PDB file, or not. The Emmental model would have been created out of one or more PDB files. The same number of PDB files will be created. The output file name will be based on the original file name with the prefix and suffix added. The verbose mode will likely report that some atoms could not be converted. These atoms whose name do not follow the PDB convention. This would be normal for the focal atom added for the NOE term, for example. TransformPDB The TransformPDB() function takes three or four arguments, apply the given transformation matrices on the specified model and writes out the resulting coordinates to one or more PDB files. Argument Type Preset Value Description partmap string name of a partition map file containing the names of PDB files model Model The Model object for an Emmental model xforms list of lists transformation matrices, one for each rigid unit prefix string "X-" to be prefixed on the original PDB file name to generate the output file name Usually, the transformation matrices are the outcome of a Monte Carlo method, in particular the Rigid Body Monte Carlo method. The transformation matrices will be obtained from a simulation with a reduced model and are now to be applied to the original all-atom model. The transformation matrices can be obtained from the transforms() function in the Yup.Methods.MonteCarlo module. This function calls the xformpdb() function in the Yup.Models.Null.PDBPartMap module which will handle multiple transforms automatically. EXAMPLES In the following, all the commands are typed into a Python interpreter. from Yup.Models.Emmental.Analyze import SCXScore, WritePDB SCXScore( M2 ) WritePDB( M2, 'MD-' ) In the above example, the model M2 was created in earlier examples, as an all-atom model from three PDB files, and fitted into the density map using a molecular dynamics-based simulated annealing procedure. The SCX score is calculated. Then, the final coordinates are written out. Since there were three original files, there will be three output files: "MD-tRNA.pdb", "MD-mRNA.pdb" and "MD-rRNA.pdb". from Yup.Models.Emmental.Analyze import TransformPDB TransformPDB( "T0001", M1, T ) In this example, we make use of the model M1, which was created from a single PDB file as coarse-grained model. It was then refined using a Monte Carlo based simulated annealing procedure using Rigid Body moves. In the example from the last section, we saved the transformation matrices returned by the AnnealMC() function in the symbol T. This is passed to the TransformPDB() function. We can expect to find an output file named "X-tRNA.pdb" which is identical to "tRNA.pdb" except for the applcation of the transformation matrices. This module makes extensive use of the functions of Yup.Tools.PDBPartMap. In its turn, PDBPartMap is based on the Yup.Tools.Brookhaven module. Utilities