Execute Command will execute any selected text, or if there is no selected text it will open a command line in the current text editor. PostDock is a new visualization tool for the analysis. Comparison of molecular docking results. It processes a docking database and displays an interactive pseudo-3D snapshot of multiple ligand docking poses such that their docking energies and docking poses are visually encoded for rapid visual assessment. The docking energies are represented by a transparency scale whereas the docking poses are encoded by a color scale. The submission includes postdock.svl, a user manual, as well as a reprint of the publication. Load a view in MOE which has the surfaces, atoms and bonds displayed as you want in the output. If you want backbone representations, then use $MOE/sample/cartoon.svl. The application is not sensitive to changes in the database (e.g. creating or deleting fields or entries); making such changes is liable to result in the application crashing. Please send any bug reports or feature requests to Set Data Fields allows the user to choose a set of data fields to be shown as text. Also a numeric field can be shown as a colour-coded square; use the Activity Indicator drop down menu to select the field.
Save and select the Picture format. Use the POV-Ray checkbox to automatically export the data to POV-Ray format. Run the ray tracer for very high quality images. The POV-Ray program is free and can be obtained from MOE requires the features of POV-Ray 3.7, which is in beta testing. The SVL modules are tied together with a script (MOE_SQL_TO_SDF.sh or MOE_SQL_TO_SDF.bat) which prompts the user for the relevant information and a SMILES column and primary key column must be specified. If the primary key is of type number then this must be converted to a varchar using oracle to_char function . If running on linux you may need to run dos2unix on the files for them to work. Browse Selected sets the browser to show only the entries that were selected when the box was checked. This means that if you are browsing a set of selected molecules and you deselect one of the entries, it will not be removed from the browser. To remove it, you will need to turn off "Browse Selected" then re-enable the option. This function allows BREED operations on aligned structures with general formula of A-B-C where B is a ring system. For n input structures, it generates all A-B-C combinations. The model covers all common reactions in P450s and has a good performance for all P450 isoforms except 2C9 and 2D6. The application will remember if you have hidden atoms in a particular chain, e.g. if you are showing only the pocket atoms from a receptor. Prompts the user to sequentially select two sets of atoms defining centroid 1. Centroid 2; the centroid distance is then calculated throughout the database. In the MOE Commands Line, type dbloop 'databasename.mdb' to run the code, which will count heavy atoms in each molecule in the first molecular field in the database. If the compounds came from an SDF file with chirality info, they will appear flat in the source MOE database. Additionally non-chiral structures are listed in the new database. This tool is very useful for saving a set of images to be made into a movie or for viewing multiple angles of a system. It saves JPEG files and can also write POVRAY if Andrew Henry's write_pov.svl function is loaded. For POVRAY you will have to edit this file to uncomment the Write_POV lines. Given a database of compounds and a SMILES/SMARTS match string , the function loops through the database and decomposes the compounds based on the scaffold match.
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