Jmol supports this CONECT convention just fine. > The way to define double bonds in the CONECT recordsof the latter is no t > straightforward if I remember well from the Chime discussions, don't > know how Jmol reads this records. This is clearly not a trivial task but it is something that would be needed whenever a CIF file is opened. Note all bonds (double or single) are shown as single rods for simplicity of viewing Return. > Well, mainly the types in which no bonds are defined, like xyz and pdb. Similarly all the scattered hydrogens have to be moved to different unit cells so that they attach to the atoms properly. The most usual formats (pdb, mol, xyz, cif) are accepted. Double-check that the structure shown is a true minimum, and not a transition. Many of these XYZ file viewers are featured molecular modeling. xyz file produced by an external computational program such as HyperChem or WebMO. Is there a way to correct this behaviour I tried to answer this question myself with a 'calculate bond order jmol' DuckDuckGo search. You can also view basic information and statistics related to atoms, bonds, molecules, etc. What I would like to happen is that the part with the orange atoms is moved up one unit cell, so that the carbon atoms attach to the blue nitrogen atoms shown at the top. Jmol, as is true for all molecular visualization software, uses molecular coordinates files for input. Some molecule file formats do not detail bond order and when I open these formats in Jmol implied (by the valency, of course) double bonds are not shown as double bonds but rather as single bonds. Even if all the atoms are shown, then chemical bonds may go between the images in different unit cells, so that bonds are not properly displayed within the unit cell.Some atoms are not shown at all if they are not symmetry-unique.What is the easiest way to extract one individual molecular image with all its bonds from a cif file? But I don't see the full molecule with all its bonds. When I open a CIF file of a crystal structure in a typical molecular editor like Avogadro, then I just see a few symmetry-unique atoms scattered around the unit cell. jmol-0.1.1 Removed the extra double-buffering that resulted from not understanding that Swing components are automatically double-buffered.
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