How to draw smooth balls (spheres) and sticks (cylinders) around my XYZ points.

Hi,

I generate the xyz coordinate of a molecule using simulation in C++. Now i have 250 atoms of xyz coordinate in one molecule. (the file attached) I want to draw the smooth surface over my atoms. So, I had written MATLAB code to draw blobby surface in my molecules. The code is following

v=load(molecule.txt);
Radius=1.5, B=-1; 
x=v(:,1);
y=v(:,2);
z=v(:,3);
[xg,yg,zg] = meshgrid(min(x)-2 : 1 : max(x)+2,min(y)-2 : 1 : max(y)+2,min(z)-2 : 1 : max(z)+2);
xd=size(xg,1);yd=size(xg,2);zd=size(xg,3);
for ii=1:xd
    for jj=1:yd
        for kk=1:zd
        blobby=0;
            for pp=1:length(v)              
                c=[xg(ii,jj,kk),yg(ii,jj,kk),zg(ii,jj,kk)] - [x(pp) y(pp) z(pp)];
                blobby=blobby+exp(B*(   (sum(c.^2 )/(Radius^2))  -1     )) ;  
            end
        G(ii,jj,kk)=blobby;
        end
    end
end

%isosurface(xg,yg,zg,G)
p=patch(isosurface(xg,yg,zg,G));
isonormals(xg,yg,zg,G,p);
set(p,'FaceColor','red','EdgeColor','none');
%daspect([2 2 2])
view(3); axis tight
camlight; lighting phong

The figure is attached for blobby parameter B = -1 and Radius =1.5

Some of the atoms are very far in my case so its not covered in single surface. If i increase the Radius and decrease B then it becomes too much smooth (it becomes sphere).

Now i wanted some new technique like to connect the bond in cylinder and atoms in sphere such that overall structure should be smooth. There is representation in vmd called CPK where i can make such image.

But i cannot make this molecule smooth. Is anyone know how to make such figures in MATLAB with good smoothness?

Thanks in advance.

[DEVANAND]

I think the first line of code must be

v=load('molecule.txt');

[Chris McComb]

Can you also provide information regarding which atoms are bonded? This will be necessary to draw the appropriate cylinders.

[ankit agrawal]

Hi Chris McComb The atoms are bonded in order of appearance in the data file. Like atom i is bonded to i+1, where i range from 1 to 249.

Answer 1

[Chris McComb]

This should do what you're looking for regarding the spheres (but see my above comment for cylinders).

% Parameters
SPHERE_RES = 20; % resolution for your spheres
SPHERE_RAD = 2.0; % radius of spheres

% Load the data
v = load('molecule.txt');

% Make base sphere data
[xb, yb, zb] = sphere(SPHERE_RES);

% Make a figure
figure;
hold on;

% Plot spheres
for i=1:1:length(v)
    surf(SPHERE_RAD*xb+v(i,1), SPHERE_RAD*yb+v(i,2), SPHERE_RAD*zb+v(i,3), 'facecolor', 'b', 'edgealpha', 0);
end

% Make sure they're smooth and shaded
light;
lighting gouraud;

[ankit agrawal]

Thank you Chris for nice replying. This was my first post in matlab central and you were the first person who replied. Thank you once again. I add this snippet in your code.

for i=1:249
    [xc,yc,zc]=cylinder2P([1,1],10,v(i,:),v(i+1,:));
    surf(xc,yc,zc);
end

where i used the cylinder2P function from here http://www.mathworks.com/matlabcentral/fileexchange/5468-cylinder-between-2-points Again i don't how to remove the edge boundary of atoms and bonds. So, that overall structure looks smooth. Can you do it?

[Chris McComb]

Happy to help! What you're seeing are the edges between panels on the surface. The way I handled that for the spheres was just to make them transparent. In your code, just replace

surf(xc,yc,zc);

with

surf(xc, yc, zc, 'facecolor', 'b', 'edgealpha', 0);

This will make the surface blue ('b'), and make the edges 0% opaque.