MS and DMS files contain dot molecular surfaces in the format output by the programs ms (written by Michael Connolly) and dms (a reimplementation available from the UCSF Computer Graphics Lab). This format is referred to as "DMS" below. Such files can also be created with the Chimera tool Write DMS.

DMS files can be used as input to sphgen, part of the DOCK suite of programs.

In Chimera, there are several ways to open DMS files. File type is indicated with a suffix (.ms or .dms, part of the filename) or a prefix (ms: or dms:, not part of the filename).

Although DMS files contain solvent-excluded molecular surfaces, they are read into Chimera as VRML models that will not update to reflect changes in any corresponding atoms. Only a single color, set when the file is opened, is used. However, a DMS surface can be associated with a particular molecule model so that the two cannot be moved or activated/deactivated for motion independently.

Surface-related Chimera menu items and the command surface only apply to MSMS surfaces, not VRML surfaces.

Write DMS

Write DMS saves part or all of a molecular surface (MSMS model) in Chimera as a DMS file.

Parameters that affect molecular surface geometry can be adjusted before writing the DMS file. Since Chimera's surface calculation method differs from that in the program dms, the dots will not coincide exactly, but various parameters can be adjusted to make the results as similar as possible:

• probe radius - the dms default and Chimera default are both 1.4 Å. If a different value had been used with dms, the Chimera setting can be changed analogously. Probe radius for an existing surface can be changed in the MSMS attributes panel, or by selecting the surface and using Selection Inspector. The probe radius to use for subsequently created surfaces can be set in the New Surfaces preferences.
• vertex density - the dms default of 1.0 gives ~5 points/Ų whereas the Chimera default is 2.0 points/Ų. Vertex density in Chimera can be adjusted as described above for probe radius.
• atomic radii - Chimera default radii differ from the dms default radii. There may not be a reason to prefer one set over the other, but if desired, the radii in Chimera can be changed to the dms default values by using Define Attribute to read the assignment file dmsrad.txt.

The MSMS surface of interest should be chosen from the pulldown list. Options:

• Save normals - include normal vectors (required by sphgen)
• Limit output to displayed surface sections - only write surface vertices that are displayed, which could include vertices that are invisible due to clipping or zoning, or that simply fall outside the current view. Display of per-atom surface patches can be controlled with the surface command or with the Actions... Surface menu.