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
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