Mesh to Molecule Command

November 28, 2006

The command meshmol creates a molecule model to render a surface mesh using cylindrical sticks. This is not a meaningful molecule -- the Chimera molecule object is just being used to make a special type of surface depiction. Other mesh display capabilities in Chimera render meshes using "lines" which are flat and do not have the 3-dimensional appearance of cylinders.


	meshmol #0 1.5

This command uses the current surface model with id number 0 to create a mesh with cylindrical links having radius 1.5.

Saving Cylindrical Meshes

The created molecule model representing the mesh can be saved using menu entry File / Save PDB.... This does not save the stick radius or colors, since there is no provision for that information in PDB format files.

The meshmol command actually makes a marker set using the volume path tracer tool. That marker set can be saved as an XML file that preserves stick radius and colors. Use menu entry Tools / Volume Data / Volume Path Tracer and then in the path tracer dialog use menu entry File / Save current marker set as.... This XML format file can only be read by Chimera.


The mesh molecule is colored to match the surface coloring which can be a single color or distinct colors for each vertex.

Kinds of Surfaces

This command works on volume, multiscale, GRASP and miscellaneous other surfaces that are created using the Chimera _surface module. The command does not work on molecular surfaces (menu Actions / Surface / Show) or on VRML surfaces.


Large surfaces. An atom is created for each surface vertex. Surfaces can easily have hundreds of thousands or millions of vertices. Molecules larger than 10,000 atoms may be time consuming to create and rendering may be slow. Saving in a PDB file will not work for molecule meshes of more than 100,000 atoms because the CONECT records used to specify the links between atoms have only a 5 digit atom serial number field.

Chimera freezes. This tool generates fake molecule models that are chemically meaningless. Chimera has code that finds small rings of connected atoms for assigning chemical atom types. For instance if you switch to sphere display for atoms it will compute atom radii based on this (carbons with different connectivities get different radii). The huge number of small rings in the fake mesh models can throw the ring calculation code into a computation that takes hours. We are working on a solution that tags fake molecular models as such.


November 28, 2006
Created command for Gabe Lander to use with Icosahedral mesh generated by hkcage command.