# This example demonstrates using MMTK and the Scientific # Python VRML2 (VRML97) visualisation module for drawing a # protein from several different angles using the camera object. # # The camera object is not available in the VRML, VPython # and VMD visualisation modules. # # The new space filling van der Waals representation (model='vdw') # is also demonstrated. [Introduced in June 2004, should be # available in the next release after Scientific Python 2.4.6] # # Written by Peter Cock # p.j.a.cock [at] warwick.ac.uk # Molecular Organisation and Assembly in Cells (MOAC) Doctoral # Training Centre, University of Warwick, CV4 7AL, UK # # from MMTK import * from MMTK.Proteins import Protein # Import the graphics module. You can substitute other graphics # module names to make the example use that module, but not # everything supports the camera object, used for view points from Scientific.Visualization import VRML2; visualization_module = VRML2 #In fact VRML, VPython and VMD do not support cameras:- #from Scientific.Visualization import VPython; visualization_module = VPython #from Scientific.Visualization import VRML; visualization_module = VRML #from Scientific.Visualization import VMD; visualization_module = VMD print "Loading protein file" #This can be any name from the MMTK database, or a PDB file. protein = Protein('insulin') #Note that by default this looks for all the atoms. Some PDB files #don't include the hydrogens, in which case MMTK will guess them. #Some PDB files don't even have the positions of the side chains, #and MMTK will not be able to guess their locations. print "Finding centre of mass and moment of inertia" center, inertia = protein.centerAndMomentOfInertia() print "Creating view points" #Use the centre of mass as the centre of the picture, with the camera #pulled back from it. # #X and Y are the axis of the screen #Y is in (-ve) and out (+ve) of the screen # #I am rotating the camera about the y-axis (which is vertical in screen) #in units of pi/2 in order to give four views (Front, Right, Back, Left) distance_away = 8.0 front_cam = visualization_module.Camera(position=[center[0],center[1],center[2]+distance_away], description="Front") right_cam = visualization_module.Camera(position=[center[0]+distance_away,center[1],center[2]], orientation=(Vector(0, 1, 0),3.14159*0.5), description="Right") back_cam = visualization_module.Camera(position=[center[0],center[1],center[2]-distance_away], orientation=(Vector(0, 1, 0),3.14159), description="Back") left_cam = visualization_module.Camera(position=[center[0]-distance_away,center[1],center[2]], orientation=(Vector(0, 1, 0),3.14159*1.5), description="Left") #Other visualisation methods ("models") you might like to try:- model_name = 'vdw' #model_name = 'tube' #model_name = 'ball_and_stick' print "Creating " + model_name + " graphic of Protein" #You can also specify colour for the whole molecule if you want, #otherwise the individual atom colours are used (Oxygen = Red, #Hydrogen = White, Sulphur = Yellow etc) graphics = protein.graphicsObjects(graphics_module = visualization_module, model = model_name) print "Creating arrows below protein" #In order to help visualise what the camera objects are doing, I #am adding some arrows in the x-z planes above and below the molecule. # #The red arrows point towards the "front" camera, green towards the #"right" camera, blue towards the "back" camera and yellow towards the #"left" camera. # d = 2.0 #distance from centre of mass (above or below) l = 2.0 #length of each arrow graphics.append(visualization_module.Arrow(center + Vector(0,-d,0), center + Vector(0,-d,l), 0.1, material=visualization_module.DiffuseMaterial('red'))) graphics.append(visualization_module.Arrow(center + Vector(0,-d,0), center + Vector(l,-d,0), 0.1, material=visualization_module.DiffuseMaterial('green'))) graphics.append(visualization_module.Arrow(center + Vector(0,-d,0), center + Vector(0,-d,-l), 0.1, material=visualization_module.DiffuseMaterial('blue'))) graphics.append(visualization_module.Arrow(center + Vector(0,-d,0), center + Vector(-l,-d,0), 0.1, material=visualization_module.DiffuseMaterial('yellow'))) print "Creating arrows above protein" graphics.append(visualization_module.Arrow(center + Vector(0,+d,0), center + Vector(0,+d,l), 0.1, material=visualization_module.DiffuseMaterial('red'))) graphics.append(visualization_module.Arrow(center + Vector(0,+d,0), center + Vector(l,+d,0), 0.1, material=visualization_module.DiffuseMaterial('green'))) graphics.append(visualization_module.Arrow(center + Vector(0,+d,0), center + Vector(0,+d,-l), 0.1, material=visualization_module.DiffuseMaterial('blue'))) graphics.append(visualization_module.Arrow(center + Vector(0,+d,0), center + Vector(-l,+d,0), 0.1, material=visualization_module.DiffuseMaterial('yellow'))) #print "Viewing front of " + model_name + " model..." #visualization_module.Scene(graphics, cameras=[front_cam]).view() #print "Viewing right of " + model_name + " model..." #visualization_module.Scene(graphics, cameras=[right_cam]).view() #print "Viewing back of " + model_name + " model..." #visualization_module.Scene(graphics, cameras=[back_cam]).view() #print "Viewing left of " + model_name + " model..." #visualization_module.Scene(graphics, cameras=[left_cam]).view() print "Viewing " + model_name + " model with all four cameras..." visualization_module.Scene(graphics, cameras=[front_cam,right_cam,back_cam,left_cam]).view() #Your VRML2 viewing program should let you switch between the #four cameras (and show you their names "Front", "Right", etc). # #For example, on Windows, using GLView 4.4 this is done using #the menu "Camera","Viewpoints" (or shortcut key F6) #Available here: http://home.snafu.de/hg/ print "Done"