VMD User's Guide

imagelighting controls, 24, 37shading and material properties, 46IMD, 51imdcommand, 100, 120Python module, 136requirements, 51implicit ligand samplingvolumetric data, 116Interactive Molecular Dynamics, 51joystickusing, 29labelcommand, 101, 120Python module, 137labels, 17categories, 44, 101delete, 44form, 43hide, 44picking with mouse, 24plotting, 45, 123show, 44text, 98lightcommand, 101, 120controlling with mouse, 24toggle, 37logfilecommand, 102, 120logging tcl commands, 102maskvolumetric data, 116masscenter of, 159of residue atoms, 119total, 161materialchanging, 108command, 102, 120methods, 39Python module, 137material properties, 99, 100matrix routinesalignment, 151identity, 150inverse alignment, 151list of, 150multiplication, 150rotation, 151trans command, 152translation, 151transpose, 150MDTools, 13measurecommand, 103, 120, 161, 162menucommand, 106, 120molecular surface, 62, 63moleculeactive, 31, 32analysis, 161best-fit alignment, 166command, 106, 110, 120data, 122deleting, 32drawn, 31fixed, 18, 31graphics, 98id, 107index, 107info, 155list, 30loading, 14, 16, 98, 164Python module, 138status, 31, 108changing, 31, 110, 155top, 31, 33, 110translation, 18molinfocommand, 110, 155keywords, 122molrepPython module, 140mouseadd or remove bonds, 24callback, 111command, 111, 120modes, 14, 18, 23, 27, 111mouse mode, 35182