Waren's example for a torsion looks pretty cool. If you're trying to make
it look like a molecule is translating in some direction, you can actually
pull this off quite nicely in photoshop. Select the thing you want create
the action shot for and copy it. Before deselecting it use the motion blur
filter, or whatever blur you want to use, and blur it out. Then paste the
original image back over the blur and maybe nudge it around a little to make
it look right and you're done!
Hope that helps some people,
Tony
On 5/5/04 10:36 AM, "Warren DeLano" <war...@delanoscientific.com> wrote:
>> 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
>
>
>
>
>
>
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