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. Most failures are on structures with
>10,000 atoms, and on the largest (~50,000 atoms), it may not be
possible to find settings that allow successful calculation of the
(but see alternatives).
Failures may even vary from platform to platform, with one computer failing
but another successfully generating the molecular surface of the
same structure using the same parameters, due to small differences in rounding.
Surface calculation fails more often on Windows than on Mac and Linux,
and more often in the 64-bit Windows version of Chimera than in the
32-bit Windows version.
Unfortunately, how to avoid a failure is also 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.
- Subdividing the problem.
The first two approaches involve breaking the problem into parts
to simplify the calculation:
- If the structure has multiple chains and it is acceptable to have
each chain enclosed in a separate surface, one can use the command
split before trying to generate
the surface. This command places the chains into different models.
For example, if the structure is originally model #0,
it will become #0.1, #0.2, etc., and in Chimera,
different models give rise to different molecular surfaces.
Potential disadvantages of using
are that previously saved positions
will cease to work, and any surface based on the original
model will not go away automatically.
- If breaking the problem into parts without splitting the model is
desired, one can use the command
surfcat to tell Chimera exactly
which atoms should be grouped together into a surface.
With this method, saved positions
will continue to work, and any previous surfaces involving the same atoms
will go away automatically. The following encloses protein chain A in its
own molecular surface:
surfcat one :.a&protein
- 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:
- The VDW radii of atoms can be
increased slightly, for example with the command:
This command also allows decreasing the radii, but increases are more likely
to circumvent the failure.
- Molecular surface
calculation parameters, namely probe radius
and vertex density, can be changed. They can be set at the time of
surface calculation with the surface
command, or prior to surface calculation in the
New Surfaces preferences.
If the main component (disconnected part) has been calculated successfully,
another approach is to select it and then use the
Selection Inspector to adjust the
associated MSMS surface
parameters after the fact.
The show disjoint surfaces setting controls whether Chimera will
try to calculate all components instead of just one.
- Alternative kinds of surfaces.
The last two possibilities generate surfaces that are not exactly the
(solvent-excluded) molecular surface,
but may suffice for visualization:
- The command molmap can be used
to simulate a density map of the atoms and display an isosurface, for example:
molmap #0&protein 4
...where larger values of the “resolution” (4 in the example)
give a smoother but slightly larger surface.
- Multiscale Models generates
one per biopolymer chain. The surfaces are essentially smoothed isosurfaces
of atom occupancy, with Resolution adjustable in the dialog.
Like molecular surfaces,
these alternative surfaces can be colored to match the underlying atoms (see
or to show associated data such as electrostatic potential (see
Color and coulombic
with the atoms option).
- 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:
repr sphere protein
- Surface area values only (no surface display).
Finally, if the goal is to obtain surface area values rather than
a displayed surface, see
from Web. This tool uses the
StrucTools server to calculate atomic
surface areas or Voronoi volumes and assigns the resulting values as atom
The output can also be written to a file. The overall total is reported
in the Reply Log, and the atomic values
and totals per residue are automatically listed as atom and residue
attributes, respectively, in the
UCSF Computer Graphics Laboratory / March 2014