Setting Up Your 3dconnexion 3d Mouse For Fusion 360 Open, highlight the program file on the list, "Run SVL". But not for any other users of MOE from that installation. Modified PCH scheme for use with RECAP fragment databases.
This script uses the SiteFinder function in an automated manner to elucidate probable binding site residues. After distance calculation, matrices of feature to feature/binding pocket centroid to feature distances are printed to the SVL commands window. In addition the list of features and the distance matrix of features will be printed in the SVL Commands Window. Only the first feature distance matrix is printed in the case that the molecule contains flipflop atoms. If there are flip flop atoms then for each possibility a different graphic object is created. These can be viewed individually using the Graphics Object Manager. Users are able to customize various aspects of visualization such as point-of-view, receptor ribbon type/color, and ligand atom color. Optionally, users can also display specific residues based on UID number and customize residue atom color. Visualization of each docked pose contained in a database will be written to a numbered 600 DPI .PNG file named after the database. For each molecule in a MOE database, load into the main MOE window and calculate ligand-receptor hydrogen bond strengths, angles and lengths in the context of the atoms in the main MOE window. Then use the DBV Browser to view the hydrogen bonds for each database entry. Subset Manager is the program for creating the subset of atoms. Changing the atatus of atoms by subset. The "machine.txt" file required by MOE/smp is generated from this selection. This imports an ASCII text file into a new MOE database, calculates the LogP for each record and then writes out another ASCII text file. This utility effectively removes those portions of a molecular surface pocket that obscure the view of the docked ligand. This file will have all of the data from the input database. Change the removeDuplicates option to 1 to enable this.
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