Surface Calculation Failures and Workarounds

Molecular surface calculations in Chimera (surface command, Actions... Surface... show in the menu) use the MSMS package and are subject to sporadic numerical failure. These failures are not very predictable, except for a tendency to occur more frequently for larger structures. Failures may even vary from platform to platform due to small differences in rounding. Surface calculation fails more often on Windows than on Mac and Linux.

One solution is to use the next-generation program ChimeraX instead of Chimera. It uses a different surface calculation method that is not subject to these failures, among other advantages, and like Chimera, it can be downloaded free of charge for noncommercial use.

The remainder of this page discusses workarounds in Chimera. Unfortunately, how to avoid a failure in Chimera is not very predictable, but anything that affects the surface shape (even quite subtly) may suffice.

The first thing to consider is whether the surface calculation has failed completely, or whether the main component (generally enclosing the structure) has been generated successfully and the failure only affects the smaller components (generally interior bubbles). If the surface of interest is shown and other components are not needed for display or calculations, surface calculation error messages can be ignored. It is possible, however, for the calculation to proceed without error messages but still generate localized defects such as interior bubbles poking through the outer surface.


  1. Subdividing the problem. The first two approaches involve breaking the problem into parts to simplify the calculation:

  2. Adjusting molecular surface parameters. The next set of approaches subtly change the surface shape or triangulation process without changing the set of atoms to be enclosed:

  3. Alternative kinds of surfaces. The last two possibilities generate surfaces that are not exactly the (solvent-excluded) molecular surface, but may suffice for visualization:

    Like molecular surfaces, these alternative surfaces can be colored to match the underlying atoms (see Color Zone and msc) or to show associated data such as electrostatic potential (see Surface Color and coulombic with the atoms option).

  4. CPK representation. Displaying all atoms as VDW spheres also gives a space-filling representation of the molecule, albeit not smoothed like a surface. For example, commands:
    show protein
    repr sphere protein
    color tan

UCSF Computer Graphics Laboratory / March 2020