To correct this oversight of ours, please use the attached code, dbvclip.svl. Run it with the MOE File Open panel ("Run SVL"). The donor, acceptor, peer donor and peer acceptor features take into account tautomerism (e.g. in carboxyl groups). The DonPeer and AccPeer features are conformation-dependent. In those conformations where a projected don/acc feature is obscured, it is eliminated. Symmetric projected peer donor feature (2.8 Angstroms away from an h-bond acceptor, oriented depending on the chemical type of the acceptor). This is a directional pharmacophore scheme with conformation-dependent projected donor and acceptor features. The donor, acceptor, projected donor and projected acceptor features take into account tautomerism (e.g. in carboxyl groups). 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.
This tool can be used for protein loop modeling in situations where MOE Homology does not work, for example in non-standard residues and covalently bound ligands. MOE's SVL is a excellent tool for computational chemistry. One of the reasons for it is that we can use SVL source code created by developers. Thus we often need to refer to the specified SVL source file. Combining 'ted_Open' and 'sym_file' commands, we can open SVL source file. This program processes all structures in a database, fragments them and writes the fragments into two new databases. Search for compounds from database B that are dis-imilar to compounds in database A, copy these into a new file, then remove duplicate finds from the results. Similarity is based on fingerprint similarity, duplicates are by SMILES, cis/trans isomerism, chirality. You can load the SVL files automatically when a MOE session starts by saving them into the $MOE/lib/svl/patch directory or $HOME/svl . New version generate more reasonable 2D structure for most of molecules. Also, revised 'Database Minimize' panel with '2D option' is now available in GUI mode. It allows seamless navigation of designs. Access to quick tools. Moving your non-mouse hand off the keyboard. Onto a 3D mouse increases productivity. Runs SiteFinder and outputs the dummy atoms of the active sites into a pdb file. Computes the distance between centroids of sets of atoms. Note that an intermediate MOE database is NOT created in this code. All files in a given directory and its subdirectories are listed, with the full path prepended to each filename. In Windows NT/2K/XP, set it up as a service using the file $MOE/bin-i4w9/rexecd (rexecd -install).
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