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

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ankit agrawal on 9 Apr 2015

Commented: Chris McComb on 10 Apr 2015

molecule.txt

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);
                        
                         forii=1:xd
                        
                         forjj=1:yd
                        
                         forkk=1:zd
                        
                         点点= 0;
                        
                         forpp=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',“红色”,'EdgeColor','none');
                        
                         %daspect([2 2 2])
                        
                         view(3); axistight
                        
                         camlight; lightingphong

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.

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ankit agrawal on 10 Apr 2015

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.

Answers (1)

Chris McComb on 10 Apr 2015

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Edited:Chris McComb on 10 Apr 2015

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
                            
                             %加载数据
                            
                             v = load('molecule.txt');
                            
                             % Make base sphere data
                            
                             [xb, yb, zb] = sphere(SPHERE_RES);
                            
                             % Make a figure
                            
                             figure;
                            
                             holdon;
                            
                             % Plot spheres
                            
                             fori=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;
                            
                             lightinggouraud;

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Chris McComb on 10 Apr 2015

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.

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