Molecules can becolored and rendered in various ways, including as secondary structure ribbons or as molecular surfaces. PMV has a sophisticatedselection mechanism based on its four level hierarchical data structure: Molecules are at the top and contain Chains, which contain Residues, whichconsist of Atoms.PMV is written in Python, an interpreted,object-oriented language that is easy to learn. While the theuser accesses PMV commands viathe menus of its Graphical User Interface, PMV records these operations in a file called' '. This log fileis a pure Python script which can be edited and/orsourced at a later time, to re-do these earlier operations. PMValso offers an extremely useful 'Undo' command for most operations.ĪDT,also known as AutoDockTools, consists of 5 specialized modules for PMV, so learning about PMV helps to understandwhat is possible with ADT. Take a look at both the ADT Tutorialand PMVTutorial. set up a ligand (the 'moving' molecule to be docked) and writeout a PDBQ file.ĪDT is an easy-to-use graphical front-end to theautomated docking software packages AutoDock and AutoGrid.set up a macromolecule (the 'fixed' molecule being docked to) andoutput a PDBQS file with solvation parameters. ![]() assign Kollman United Atom charged to a protein or peptide, orDNA or RNA.
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