> is there any way of showing movement of a > molecule in a static image, for example as speed lines or a > blur between the two states? If this makes any sense please > let me know if you have some ideas!Mike,
Motion blur in PyMOL is possible, but the process is a bit tedious. You need to create separate states for the "moving" portion of the molecule with different transparency. Also, it doesn't look right from every vantage point. Here is an example image with the accompanyning script: http://www.delsci.com/img/blur.png # get some object fragment phe, blur # create multiple states for a in range(2,21):\ cmd.create("blur","blur",1,a) # rotate the bond in each state for a in range(1,21):\ cmd.frame(a) \ cmd.edit("blur////cb","blur////ca") \ cmd.torsion((a-1)/1.5) # show sticks only hide everything,blur show sticks,blur # adjust stick transparency for each state for a in range(1,21):\ cmd.set("stick_transparency",(20.0-a)/20,"blur",a) # show all states set all_states, on # adjust transparency settings set ray_transparency_shadows, off set ray_transparency_specular, off # set a good view set_view (\ 0.962713897, -0.181692749, -0.200423554,\ -0.189038053, -0.981805086, -0.017973814,\ -0.193509772, 0.055190988, -0.979543626,\ 0.000000393, -0.000000030, -22.716976166,\ -0.364352912, 0.062815413, 0.104579724,\ 12.716978073, 72.716979980, 0.000000000 ) # now ray trace ray # END SCRIPT Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
