MS and DMS Files

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:

There are several ways to start Write DMS, a tool in the Structure Editing category.

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

Save writes a file using the specified name and location and dismisses the dialog, while Close simply dismisses the dialog. Help opens this manual page in a browser window.

UCSF Computer Graphics Laboratory / November 2008