Contains all the code for generating the order of the dockings. The IMP.em2d Python package contains a number of utility modules: This utility can be used to convert one or more EM images from Spider format to JPG. The scoring is done keeping in memory only the number of images specified by the parameter.Įmagefit_score structure.pdb l 3.6 20 5 100Ĭonvert_spider_to_jpg: Image conversion utility for EMageFit. This parameter is used to avoid running out of memory when the number of images used for scoring a model is large. For images of poor quality, with no distinguishable features, values of 10-15 may be used. For the published EMageFit benchmark a value as low as 2 was used, as the results are not very different from using lower resolutions. The larger the value, the blurrier the projections generated. The model is downsampled to this value of the resolution before projecting it. The resolution used to generate the projections.The number of projections used for the coarse registration step of the scoring.To score a model the parameters required are: It is useful for comparing models obtained by other sampling algorithms apart from the one described in the EMageFit paper. The help of the script gives the parameters required, and a typical command is:Įmagefit -exp config_step_3.py -o domino_solutions.db -wcl clusters.db 1Įmagefit_score: Scores a model using EM images. The only function that needs to be adapated for a different docking program is parse_hex_transform(), which both of them use.Įmagefit_cluster: Performs clustering of the solutions stored in a database file. emagefit also calls the functions read_hex_transforms() and filter_docking_results().This class can be replaced with another class that provides a dock() method that saves the results to a file. The class HexDocking is used only from emagefit and uses the dock() method.The script can be modified to use any docking program, by making a couple of changes: The script can be used as a standalone program to perform a docking or write the solutions. This uses HEXDOCK in text mode to perform a docking of a subunit (the ligand) into another subunit (the receptor). This script performs Docking, Monte Carlo optimization, gathering of solutions from the Monte Carlo runs, DOMINO sampling, and finally writing the resulting models.Įmagefit_dock: Docking using the HEXDOCK program
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