![]() Here some clarifying words about these ‘strange’ sticks: How does the connect for double bond work?ĭo I need to put it twice or just once? and which one? In addition somethings it doesn’t pick up the connect and form a double bond.Īnyone want to share a pdb with benzene that shows the double bonds? What one has to do is to modify the PDB file: take all atoms with double bonds and name the 2nd atom 2x, e.g.: CONECT 31 49 55 55 10Ītom No. In other words, there must be an algorithm inside Avogadro, which can find double bonds. So, it seems to me that there is no way to determine double bonds from a Avogadro PDB file alone (from the CONECT identifiers). Let’s see, may be there is a solution to treat both …. To explicitly show double bonds, there must be entries in the PDB file in the form: CONECT 31 49 55 55 10Ītom No. This is not the case for the PDB IO addon (so far). ![]() However, since it dissapears in the picture, it is not such a big problem.ĭouble bonds and Avogadro: Avogadro probably has an algorithm included, which permits determining double bonds. You cannot remove it or make it invisible. As it is expailned somewhere on the top, the extra atom is the representative ball of the dupliverts structure. Missing double bonds: You have to cross check the option ‘bonds’ in the file dialog.Įxtra carbon atoms: ‘the extra atoms’ are always visible in the 3D scene, but they dissapear in the rendered picture. Please, can you supply the version of Blender and the addon you are using? Furthermore, can you send the PDB file for testing? There shouldn’t be a problem with Avogadro, I daily use their PDB files. Most importantly is: does the pdb_to_fbx conversion now work in your case now? Īnyway, the re-import needs some further review. The only problem I have is that somehow I cannot re-import the fbx file into Blender. Attention, the fbx file size becomes very large for ball=‘2’! With this, all works (all balls, 0 to 2), well at least in my case (Linux Ubuntu 13.10, 64Bit). I’m very busy atm.īpy.ops.import_mesh.pdb(filepath=file_pdb, filter_glob="*.pdb", use_center=True, use_camera=False, use_lamp=False, ball='0', mesh_azimuth=32, mesh_zenith=32, scale_ballradius=1, scale_distances=1, atomradius='0', use_sticks=True, use_sticks_type='0', sticks_subdiv_view=2, sticks_subdiv_render=2, sticks_sectors=20, sticks_radius=0.2, sticks_unit_length=0.05, use_sticks_color=True, use_sticks_smooth=True, use_sticks_bonds=False, sticks_dist=1.1, use_sticks_one_object=True, use_sticks_one_object_nr=200, datafile="")īpy.ops.export_scene.fbx(filepath=file_fbx, object_types=, use_anim=False)
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