 # Creating a smooth surface in 3D

Dear mpl friends,

My objective is to create a molecular surface using matplotlib. I used the
snippet pasted below to create a series of spheres (attached png), drawn
using the atom attributes (their positions and radius). From here, I would
like to create a smooth surface which can depict the shape of the molecule
surface (curves,cavities etc). Based on examples in net, I get a mixed
feeling that either triangulation or making 3D grids are some directions to
proceed. If anyone has some suggestions or better protocols for such task
with some example data, it would be of great help to me.

fig = plt.figure(figsize=(6,6),dpi=140)

# Define spherical coordinates

u, v = np.mgrid[0:2*np.pi:20j, 0:np.pi:10j]

S = np.cos(u)*np.sin(v)

C = np.sin(u)*np.sin(v)

T = np.cos(v)

ax1.plot_wireframe(R*S+P,R*C+P,R*T+P,color='r',alpha=0.4)

Bala

···

--
C. Balasubramanian
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mplot3d is good for real simple 3d scenes, but it falls apart when you
start composing things like this. You might want to consider using
something like glumpy or mayavi for better results. There are some
discussions in the past on the problems inherent in creating spheres in
mplot3d. There are some interesting solutions, but they get fairly complex
pretty quickly.

Cheers!
Ben Root

···

On Mon, May 28, 2018 at 8:16 AM, Bala subramanian <bala.biophysics at gmail.com > wrote:

Dear mpl friends,

My objective is to create a molecular surface using matplotlib. I used the
snippet pasted below to create a series of spheres (attached png), drawn
using the atom attributes (their positions and radius). From here, I would
like to create a smooth surface which can depict the shape of the molecule
surface (curves,cavities etc). Based on examples in net, I get a mixed
feeling that either triangulation or making 3D grids are some directions to
proceed. If anyone has some suggestions or better protocols for such task
with some example data, it would be of great help to me.

fig = plt.figure(figsize=(6,6),dpi=140)

# Define spherical coordinates

u, v = np.mgrid[0:2*np.pi:20j, 0:np.pi:10j]

S = np.cos(u)*np.sin(v)

C = np.sin(u)*np.sin(v)

T = np.cos(v)

ax1.plot_wireframe(R*S+P,R*C+P,R*T+P,color='r',alph
a=0.4)

Bala

--
C. Balasubramanian

_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
https://mail.python.org/mailman/listinfo/matplotlib-users

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Thanks for the inputs. After some efforts, I managed to create the surface
by generating vertex and faces using an external program and mpl tools.

ax1.plot_trisurf(x, y, z, triangles=faces,color='w', lw=10)

ax1.scatter3D(x, y, z, c= cols,s=10)

However, i am now trying to figure out the simple way to color the
triangles using the vertex colors.

For each vertex, I have assigned a color (ranges from blue to red) which in
my case represents a calculated property. So basically I have a color array
(cols in the above snippet) that I passed to the scatter function. I would
like to know how I can color the triangle by interpolating to the colors of
the vertex it belongs to. The available examples in net show the usage of
colormaps. In my case, the triangles should adopt vertex colors.

Any tricks to achieve this could be of much help. I have attached a sample
figure, which i believe, could better elucidate the problem.

···

On Mon, May 28, 2018 at 3:19 PM, Benjamin Root <ben.v.root at gmail.com> wrote:

mplot3d is good for real simple 3d scenes, but it falls apart when you
start composing things like this. You might want to consider using
something like glumpy or mayavi for better results. There are some
discussions in the past on the problems inherent in creating spheres in
mplot3d. There are some interesting solutions, but they get fairly complex
pretty quickly.

Cheers!
Ben Root

On Mon, May 28, 2018 at 8:16 AM, Bala subramanian < > bala.biophysics at gmail.com> wrote:

Dear mpl friends,

My objective is to create a molecular surface using matplotlib. I used
the snippet pasted below to create a series of spheres (attached png),
drawn using the atom attributes (their positions and radius). From here, I
would like to create a smooth surface which can depict the shape of the
molecule surface (curves,cavities etc). Based on examples in net, I get a
mixed feeling that either triangulation or making 3D grids are some
directions to proceed. If anyone has some suggestions or better protocols
for such task with some example data, it would be of great help to me.

fig = plt.figure(figsize=(6,6),dpi=140)

# Define spherical coordinates

u, v = np.mgrid[0:2*np.pi:20j, 0:np.pi:10j]

S = np.cos(u)*np.sin(v)

C = np.sin(u)*np.sin(v)

T = np.cos(v)

ax1.plot_wireframe(R*S+P,R*C+P,R*T+P,color='r',alph
a=0.4)

Bala

--
C. Balasubramanian

_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
https://mail.python.org/mailman/listinfo/matplotlib-users

--
C. Balasubramanian
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I managed to interpolate the face colors based on vertex property following
the example given below.

https://stackoverflow.com/questions/24218543/colouring-the-surface-of-a-sphere-with-a-set-of-scalar-values-in-matplotlib

I am just updating here so as to direct anyone looking trying similar
stuff. Thanks.

···

On Fri, Jun 1, 2018 at 10:52 AM, Bala subramanian <bala.biophysics at gmail.com > wrote:

Thanks for the inputs. After some efforts, I managed to create the surface
by generating vertex and faces using an external program and mpl tools.

ax1.plot_trisurf(x, y, z, triangles=faces,color='w', lw=10)

ax1.scatter3D(x, y, z, c= cols,s=10)

However, i am now trying to figure out the simple way to color the
triangles using the vertex colors.

For each vertex, I have assigned a color (ranges from blue to red) which
in my case represents a calculated property. So basically I have a color
array (cols in the above snippet) that I passed to the scatter function. I
would like to know how I can color the triangle by interpolating to the
colors of the vertex it belongs to. The available examples in net show the
usage of colormaps. In my case, the triangles should adopt vertex colors.

Any tricks to achieve this could be of much help. I have attached a sample
figure, which i believe, could better elucidate the problem.

On Mon, May 28, 2018 at 3:19 PM, Benjamin Root <ben.v.root at gmail.com> > wrote:

mplot3d is good for real simple 3d scenes, but it falls apart when you
start composing things like this. You might want to consider using
something like glumpy or mayavi for better results. There are some
discussions in the past on the problems inherent in creating spheres in
mplot3d. There are some interesting solutions, but they get fairly complex
pretty quickly.

Cheers!
Ben Root

On Mon, May 28, 2018 at 8:16 AM, Bala subramanian < >> bala.biophysics at gmail.com> wrote:

Dear mpl friends,

My objective is to create a molecular surface using matplotlib. I used
the snippet pasted below to create a series of spheres (attached png),
drawn using the atom attributes (their positions and radius). From here, I
would like to create a smooth surface which can depict the shape of the
molecule surface (curves,cavities etc). Based on examples in net, I get a
mixed feeling that either triangulation or making 3D grids are some
directions to proceed. If anyone has some suggestions or better protocols
for such task with some example data, it would be of great help to me.

fig = plt.figure(figsize=(6,6),dpi=140)

# Define spherical coordinates

u, v = np.mgrid[0:2*np.pi:20j, 0:np.pi:10j]

S = np.cos(u)*np.sin(v)

C = np.sin(u)*np.sin(v)

T = np.cos(v)

ax1.plot_wireframe(R*S+P,R*C+P,R*T+P,color='r',alph
a=0.4)

Bala

--
C. Balasubramanian

_______________________________________________
Matplotlib-users mailing list
Matplotlib-users at python.org
https://mail.python.org/mailman/listinfo/matplotlib-users

--
C. Balasubramanian

--
C. Balasubramanian
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