Hi Karin, Yes, I did change Chimera Surface_Model to only support triangulated surfaces, eliminating the quadrilateral surfaces. I'm amazed that you found the quadrilateral capability. The new code does allow displaying quadrilaterals in a different way -- and in fact can display pentagons, hexagons and other shapes with the additions made to Chimera 1.2255. I eliminated the old quadrilateral support when I added these new features because the code was too complex and I did not expect anyone was using it. The new Surface_Model only allows surface specifications with triangles. If you have quadrilaterals it is easy to turn it into triangles. For a quadrilateral with vertices 1, 2, 3, 4 just make two triangles with vertices 1, 2, 3 and 1, 3, 4. The new Surface_Model allows hiding any triangle edges when displaying with mesh style. When you divide the quadrilateral into 2 triangles you can hide the introduced quadrilateral diagonal. Below is an example of making a cube with 6 faces in the old (1.2199) and new (1.2255) ways. At the end there is a routine to turn quadrilateral lists into triangle lists and an edge mask. The new Surface_Model allows displaying meshes with pentagons or hexagons, or any arbitrary set of triangle edges, for example http://www.cgl.ucsf.edu/chimera/experimental/hkcage/cage.html Also I added a new "square mesh" option to the Chimera volume viewer dialog that shows contour meshes where just the intersection of the grid planes perpendicular to x, y and z axes with the contour surface are shown. This is the kind of mesh the program O uses. I hope the new Surface_Model interface is not too troublesome to use. The new edge masking capability makes it more powerful, but also more complex. Tom ----- Python code quads.py follows: # ----------------------------------------------------------------------------- # Create a cube surface model using quadrilaterals with Chimera 1.2199. # def cube_old_style(): from _surface import Surface_Model s = Surface_Model() # Cube corner xyz positions. vlist = ((0,0,0), (0,0,1), (0,1,0), (0,1,1), (1,0,0), (1,0,1), (1,1,0), (1,1,1)) # 4-tuples of vertex list indices. qlist = ((0,4,5,1), (0,2,6,4), (0,1,3,2), (7,3,1,5), (7,6,2,3), (7,5,4,6)) from Numeric import array, Float32 vlist_f32 = array(vlist, Float32) # add_group() requires Float32 vertices rgba = (1,1,1,1) # white g = s.add_group(vlist_f32, qlist, rgba) g.set_display_style(g.Mesh) from chimera import openModels openModels.add([s]) # Add model to list of open models. # ----------------------------------------------------------------------------- # Create a cube surface model using triangles with Chimera 1.2255. # def cube_new_style(): from _surface import Surface_Model s = Surface_Model() # Cube corner xyz positions. vlist = ((0,0,0), (0,0,1), (0,1,0), (0,1,1), (1,0,0), (1,0,1), (1,1,0), (1,1,1)) # 3-tuples of vertex indices specify triangles, 2 for each of 6 cube faces. tlist = ((0,4,5), (5,1,0), (0,2,6), (6,4,0), (0,1,3), (3,2,0), (7,3,1), (1,5,7), (7,6,2), (2,3,7), (7,5,4), (4,6,7)) # Bit mask: 8 = show triangle # 4 = show triangle edge from vertex 0 to vertex 1 # 2 = show triangle edge from vertex 1 to vertex 2 # 1 = show triangle edge from vertex 2 to vertex 0 b = 8 + 2 + 1 hide_diagonals = (b,b,b,b,b,b,b,b,b,b,b,b) from Numeric import array, Float32 vlist_f32 = array(vlist, Float32) # add_group() requires Float32 vertices rgba = (1,1,1,1) # white g = s.add_group(vlist_f32, tlist, rgba) g.set_display_style(g.Mesh) g.set_triangle_and_edge_mask(hide_diagonals) from chimera import openModels openModels.add([s]) # Add model to list of open models. # ----------------------------------------------------------------------------- # Convert quadrilaterals to triangles with appropriate edge mask. # def quadrilaterals_to_triangles(qlist): tlist = [] for v0,v1,v2,v3 in qlist: tlist.append((v0,v1,v2)) tlist.append((v2,v3,v0)) emask = 8 + 2 + 1 edge_mask = [emask] * len(tlist) return tlist, edge_mask