Fig. 1

Comparing topology visualization using ProLego (a) and PTGL (b) for the case of photosynthetic reaction centre (Photosystem1 (PDB Id: 1JB0; chain: L)). The chain an anit-parallel beta sheet at the N-terminal followed by seven alpha-helices. Fig a.ii, shows a cartoon representation of protein chain using VMD. In linear topology (a.iv) strands are represented as triangles (with relative orientation as up/down triangle) and helices are represented as rectangle. The length of helical rectangles scaled as per number of residues in corresponding helix. The protein chain is represented as red to green to blue as passes from N to C terminal. The linear lines, connecting secondary structure (SS) blocks shows chain connectivity, whereas the arc lines represent spatial connectivity and type of SS contact (colour coded as labelled in Additional file 1: Table S4). The secondary structure contact map (a.i), shows all spatial contact between pairs of SS. A 3D carton representation (VMD generated a.ii) and 2D topology cartoon (a.iii) plot is generated from ProLego. The 2D ProLego cartoon shows contact between two SS blocks by red dotted lines and chain connectivity by black continuous line. Figure b, shows the topology representation of same protein generated using protein topology graph library (http://ptgl.uni-frankfurt.de/api/index.php/pg/1jb0/L/albe/json), the alpha-beta graph. The graph represents SSEs from N to C terminal in left to right fashion. Helices are represented as circles and stands as rectangles. PTGL considers, 3₁₀ helices also in total helix, hence the addition of 1st and 7th helix, giving total number of helix to 9 instead of 7 alpha-helix as per ProLego in this protein. PTGL misses the N-terminal sheet, which is represented as up-down triangle (for anti-parallel orientation) in case of ProLego