Chimera Commands Index

meshmol surf-model stick-radius

The meshmol command creates a molecule model from a surface. This allows mesh display as cylindrical sticks, whereas surface model meshes can only be shown as lines. Meshmol works on all kinds of surface models, but not on surfaces in VRML models. See also: hkcage, shape, volume, struts, set subdivision, Cage Builder, Volume Tracer

Surf-model is the model number of the surface, optionally preceded by #.

A new molecule model is created in which the "bonds" (the mesh lines in the surface model) are shown as sticks of the specified stick-radius. It is colored to match the surface coloring, which could be a single color or different colors for different vertices. The molecule model is also a marker set.

Advantages of treating a surface as a molecule include the ability to display sticks, as mentioned above, and to perform other operations available for atoms and bonds, including saving coordinates to a file. Further, since the molecule model is a marker set, Volume Tracer can be used to control its display and save it as a marker file. Marker files include colors and radii in addition to coordinates.

Disadvantages relate to the creation of physically unreasonable molecules with very large numbers of atoms and bonds. Chimera performs chemical perception, which may take up to hours in the presence of huge numbers of small rings. This essentially freezes the program. Any operations that trigger chemical perception should be avoided after meshmol is used, such as using the ball-and-stick or sphere representations or adding hydrogens, even to other molecules. Atoms and bonds use more memory than surface points and mesh lines, and rendering large surfaces as cylinders may take a long time. Mesh molecules with more than 100,000 atoms cannot be saved as PDB files because the CONECT records only allow 5-digit atom serial numbers.