cylinder.m

%Created by Yao-Wang Li, at Aug. 04, for cylinder simulation.

BoxSizeInPixel = 256;
PixelSize = 1.32;                     %A/pixel
BoxSize = round(BoxSizeInPixel * PixelSize);   %Box size in A  
BoxHalf = BoxSize/2 ;
rise = 4.8;
BoxHalf = BoxHalf - mod(BoxHalf,rise);
D = 100; 
r = D/2;

xy = zeros(1,2);

for i = [-r:5:r]
for j = [-r:5:r]
  r_square = r*r;
  if (i^2 + j^2 <= r_square)
    xy = [xy;i,j];
  else
    continue;
   end
 end
end
xy(1,:) = [];

num = rows(xy);
z = zeros(num,1);
coors = [xy,z];

for i = [-BoxHalf:rise:BoxHalf]
  if (i != 0)
    z = zeros(num,1);
    z(:) = i;
    tmp = [xy,z];
    coors = [coors;tmp];
  else
    continue;
  end
end

scatter3(coors(:,1),coors(:,2),coors(:,3));



 
fid = fopen('cylinderCoors.txt', 'wt');
for i = 1:size(coors,1)
    fprintf(fid, '%-0.4f \t', coors(i,:));
    fprintf(fid, '\n');
end
fclose(fid);


%Create pdb file
Helixpdb = fopen('cylinder.pdb','w');
fprintf(Helixpdb, '%-6s\t %-40s\n', 'HEADER', 'GENERATED by Octave script.');
fprintf(Helixpdb, '%-6s\t %-40s\n', 'AUTHOR', 'YAO-WANG LI');
fprintf(Helixpdb, '%-6s\n', 'HEADER');
 

% the e2pdb2mrc.py read 12:14, 6:11, 22:26, 30:38, 38:46,46:54
for i = 1:rows(coors)
    fprintf(Helixpdb,'%-5s%6d%3s%6s%1c%5d    %-8.3f%-8.3f%-8.3f\n', 'ATOM', i, 'N', 'HIS', 'A', 1, coors(i,1), coors(i,2), coors(i,3));
    fprintf(Helixpdb, '%-6s\n', 'TER');
end

fprintf(Helixpdb, '%-6s\n', 'END');
fclose(Helixpdb);