Surfaces in Chimera

Group meeting.
October 27, 2008

Miscellaneous improvements in creating surfaces, controlling surface appearance, measuring surfaces, rendering speed (OpenGl vertex buffer objects, 2x-3x faster). Unified molecular and volume surfaces.

MSMS standalone program, avoids crashing Chimera

Outputs surface areas of components. Use split components shortcut Sc to make components separately selectable.

Surface 1fav.pdb, category main, probe radius 1.4, vertex density 2
  2 connected surface components
  Total solvent excluded surface area = 7793.01
    component areas = 7765.1, 27.9083
  Total solvent accessible surface area = 9851.23
    component areas = 9851.21, 0.0244145

MSMS surface.

Second MSMS surface component.

Hide individual triangles with mouse clicks to clean up edge.

Molmap command makes low resolution molecular surfaces

Use gridSpacing argument to improve smoothness.
(1fav, molmap #0,2,3 5 gridSpacing .5, raise volume threshold, colorzone)

Edge-on transparency (script)

Edge-on view of transparent surface patch is more opaque than face-on view.

Actions menu works on selected surfaces

Multiscale, color, show ribbon, surface transparency, focus, up-down arrow keys.

Measure inertia of surface or pdb model

Can resize with mouse mode (shortcut sz).
Can select through mesh.

Measure surface to surface distance statistics (script)

Slab thickness mean 361.59, sdev 119.13, min 113.35, max 786.12, samples 4522
Slab thickness mean 213.45, sdev 43.224, min 40.387, max 313.46, samples 4689

Remove small blobs ("dust") from volume surfaces (script)

Front center rotation mode for rotating about surface virus spike

Contour lines for volume planes

Automatic tracing of lipid surfaces in electron microscope tomography