How can I generate a nice picture by pymol?
This is the online supplemental wiki for "An Introduction to Biomolecular Graphics" PLoS Comput Biol (2010) 6(8): e1000918. doi:10.1371/journal.pcbi.1000918.
Cool PyMOL-generated Images and their Scripts.
# antialias =1 smooths jagged edges, 0 turns it off set antialias = 1 # Larger values of ambient make the image brighter set ambient=0.3 # Larger values of direct eliminates shadows set direct=1.0 set ribbon_radius =0.2 # cartoon_highlight_color will give a separate color to edges of secondary structural elements. set cartoon_highlight_color =grey50 # ray_trace_mode=1 makes a black outline around the secondary structural elements set ray_trace_mode=1 # stick_radius -adjust thickness of atomic bonds set stick_radius = 0.2 # mesh_radius -to adjust thickness of electron density contours set mesh_radius = 0.02 # bg_color --set the background color bg_color white # load pdb file and give it an object name load https://shaker.umh.es/computing/4aq9-ligands.pdb # hide nonbonded atoms (i.e. waters) hide nonbonded # show cartoon ribbons show cartoon # Hide the default line representation of atomic bonds hide lines # Use standard helix, strand, and loop representations # other possibilities: cartoon loop, cartoon rect, # cartoon oval, and cartoon tube set cartoon_tube_radius, 0.2 # Make fancy helices with ridge on the edges like # molscript does # 1 is on. 0 is off. set cartoon_fancy_helices=1 set cartoon_cylindrical_helices=0 # Make the strands flat=1 or pass through CA positions=0 # Set to 0 when showing side chains from a strand set cartoon_flat_sheets = 1.0 # Draw the loops smooth=1 or pass through CA positions=0 # Set to 0 when showing side chains from a loop set cartoon_smooth_loops = 0 # Example loading a protein and its electron density map # fetch 1cll load https://shaker.umh.es/computing/4aq9-ligands.pdb # set object's color to colorName set label_color, blue, coco # set the label size to 10pt set label_size, 10 # set object's color to colorName set label_color, colorName, object # label_position sets the offset of the label relative to the atomic position. # Offsets the labels 3 Å in X, 2 in Y and 1 in Z set label_position,(3,2,1)