Hi John,
what you need is a "discrete" object, not only because of the coloring,
but also because you say the number of particles is not the same for
each state.
Try to apply two modifications:
1) "discrete" argument for "load":
cmd.load(file, "movie", discrete=1)
2) "state" argument for "select":
cmd.select("particle", "id "+str(particle_index+1), state=i)
I hope this will work :)
Cheers,
Thomas
John Russo wrote, On 08/31/12 09:14:
> Hi,
> I have been fighting with this problem for some time now,
> and I think it is time to try to ask to more experienced users.
>
> What I want to achieve is really simple. I want to make a movie
> with only spheres. At every frame each sphere has also a scalar
> property (e.g. local density) which is used to color the sphere
> accordingly.
>
> So my input are a series of xyz files, and a corresponding series
> of files holding the value of that scalar for each particle.
>
> What I'm doing now is:
>
> *) loading all the xyz file into different states
> *) creating a frame from each of these states
> *) loop on the different frames and color the spheres
> according to the field
>
> My problem is in this last point, as I cannot find a way to
> tell pymol to colour each sphere only for that frame, and
> I always end up with a movie where the colour of the spheres
> is fixed by the last frame.
>
> Here is some pseudo code for what I'm doing:
>
>
> for file in file_list:
> cmd.load(file,"movie")
>
> cmd.mset("1 -%d" % cmd.count_states())
>
> for i in range(1,cmd.count_states()+1):
> name="%d" % (i)
>
> cmd.frame(i)
>
> scalar=readField(scalar_field[i])
>
> for particle_index,s in enumerate(scalar):
>
> cmd.select("particle","id "+str(particle_index+1))
> cmd.color(custom_color[s],"particle")
>
>
> cmd.scene(name,"store")
> cmd.mview('store',name)
>
>
> One last thing, the number of particles is not the same for every state.
>
> I hope somebody can help me. Thanks,
>
> John
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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