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. See also: Sphgen sphere files

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 in Chimera as a DMS file, such as used by the sphgen module of DOCK. See also: Sphgen sphere files

Since Chimera's surface calculation method differs from that in the program dms, the dots in DMS files produced in the two different ways will not coincide exactly, but parameters can be set to make the results as similar as possible. For example, the dms default density setting of 1.0 gives ~5.0 dots/Ų whereas the Chimera default is 2.0 dots/Ų. The vertex density in Chimera can be specified in the surface command or changed in a pre-existing surface with setattr, for example:

Command: setattr s density 5

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 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.

• probe radius - the dms default and Chimera default are both 1.4 Å
• show disjoint surfaces - whether to calculate disconnected blobs of surface such as inside bubbles; omitting them simplifies the surface and may be a good idea, unless the binding site of interest is completely enclosed

Command: setattr s probeRadius 1.5
Command: setattr s allComponents false

Finally, the 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.

Limitation

A limitation of the DMS files from Write DMS (not relevant to sphgen use, however) is that all points are labeled C for contact surface, whereas S should be used for saddle surface and R for reentrant surface. This limitation comes from the MSMS package that Chimera uses to calculate molecular surfaces, which reports all points as type 3 (contact) although types 1 (toric reentrant) and 2 (spheric reentrant) are also documented.