FR3D_InteractionMap(File) puts a dot at the center of each nucleotide in File, colored by the number of interactions the nucleotide has (blue means zero, red is the most). The C1' atom of each nucleotide is connected to the C1' atom of the next nucleotide by a black line. Interactions are shown between centers of nucleotides. WC-WC interactions (category 1) are shown by red lines, non-canonical planar interactions by green, typical sequential stacking (category 21) by dark blue, and typical cross-strand stacking (categories 22, 23) by light blue. File can be, for example, '1s72' or File(3). The vector DL, if specified, controls what is displayed: DL(1) = 1; % plot geometric center DL(2) = 1; % show cWW bonds DL(3) = 1; % show other planar bonds DL(4) = 1; % show 35 and 53 stacking DL(5) = 1; % show 33 and 55 stacking DL(6) = 1; % connect glycosidic atoms
0001 % FR3D_InteractionMap(File) puts a dot at the center of each nucleotide 0002 % in File, colored by the number of interactions the nucleotide has (blue 0003 % means zero, red is the most). The C1' atom of each nucleotide is 0004 % connected to the C1' atom of the next nucleotide by a black line. 0005 % Interactions are shown between centers of nucleotides. WC-WC 0006 % interactions (category 1) are shown by red lines, non-canonical planar 0007 % interactions by green, typical sequential stacking (category 21) by 0008 % dark blue, and typical cross-strand stacking (categories 22, 23) by light 0009 % blue. 0010 % File can be, for example, '1s72' or File(3). 0011 % The vector DL, if specified, controls what is displayed: 0012 % DL(1) = 1; % plot geometric center 0013 % DL(2) = 1; % show cWW bonds 0014 % DL(3) = 1; % show other planar bonds 0015 % DL(4) = 1; % show 35 and 53 stacking 0016 % DL(5) = 1; % show 33 and 55 stacking 0017 % DL(6) = 1; % connect glycosidic atoms 0018 0019 function [void] = FR3D_InteractionMap(File,DL,NTList) 0020 0021 if nargin < 1 0022 fprintf('Please specify a filename, e.g. FR3D_InteractionMap(''1s72'')\n'); 0023 end 0024 0025 % if File is a text string (filename), load the file and display 0026 0027 if strcmp(class(File),'char'), 0028 Filename = File; 0029 File = zGetNTData(Filename,0); 0030 end 0031 0032 % if NTList is a cell array of numbers, look up the indices 0033 0034 if nargin > 2, 0035 0036 if strcmp(class(NTList),'char'), 0037 NTList = {NTList}; 0038 end 0039 0040 if strcmp(class(NTList),'cell'), 0041 Indices = zIndexLookup(File,NTList); 0042 else 0043 Indices = NTList; 0044 end 0045 0046 else 0047 0048 Indices = 1:length(File.NT); 0049 0050 end 0051 0052 if nargin < 2 0053 DL(1) = 1; % plot geometric center 0054 DL(2) = 1; % show cWW bonds 0055 DL(3) = 1; % show other planar bonds 0056 DL(4) = 1; % show 35 and 53 stacking 0057 DL(5) = 1; % show 33 and 55 stacking 0058 DL(6) = 1; % connect glycosidic atoms 0059 end 0060 0061 %----------------------------------------------------------------------- 0062 figure(1) 0063 clf 0064 0065 set(gcf,'Renderer','OpenGL'); 0066 0067 for a = 1:length(Indices), % Loop through nucleotides 0068 k = Indices(a); 0069 i = abs(File.Edge(k,Indices)); 0070 ii = find((i < 30) .* (i > 0)); 0071 iii = Indices(ii); 0072 ni(k) = length(iii); % number of interactions 0073 0074 e = File.NT(k).Center; 0075 if DL(1) > 0, 0076 scatter3(e(1),e(2),e(3),6,ni(k)+1,'filled'); % plot geometric center 0077 else 0078 scatter3(e(1),e(2),e(3),1,ni(k)+1,'filled'); % plot dots at least 0079 end 0080 hold on 0081 0082 c = 0; 0083 0084 for j = 1:length(iii), 0085 if iii(j) < k, % only plot once 0086 f = File.NT(iii(j)).Center; 0087 inter = abs(fix(File.Edge(k,iii(j)))); 0088 if inter == 1, 0089 if DL(2) > 0, 0090 plot3([e(1) f(1)],[e(2) f(2)],[e(3) f(3)],'b'); % WC-WC 0091 end 0092 c = c + 1; 0093 elseif abs(inter) < 15, 0094 if DL(3) > 0, 0095 plot3([e(1) f(1)],[e(2) f(2)],[e(3) f(3)],'c'); % other planar 0096 end 0097 c = c + 1; 0098 elseif (inter == 21), 0099 if DL(4) > 0, 0100 plot3([e(1) f(1)],[e(2) f(2)],[e(3) f(3)],'y'); % 35 or 53 stacking 0101 end 0102 c = c + 1; 0103 elseif (inter == 22) | (inter == 23), 0104 if DL(5) > 0, 0105 plot3([e(1) f(1)],[e(2) f(2)],[e(3) f(3)],'y'); % 33 or 55 stacking 0106 end 0107 c = c + 1; 0108 end 0109 end 0110 end 0111 0112 if DL(6) > 0, 0113 g = File.NT(k).Fit(1,:); 0114 h = File.NT(max(1,k-1)).Fit(1,:); 0115 if sum((g-h).^2) < 200, % reasonable distance 0116 plot3([g(1) h(1)],[g(2) h(2)],[g(3) h(3)],'k') % connect glycosidics 0117 end 0118 end 0119 0120 end 0121 0122 set(gcf,'Renderer','painters'); 0123 axis off 0124 0125 rotate3d on