> 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
  




Reply via email to