-- not implemented in Chimera --

Dms is available on:


dms - calculate a molecular surface


dms pdbfile [ -a ] [ -d density] [ -g logfile ] [ -i sitefile ] [-n] [-w radius ] [-v] -o outfile


Dms calculates the molecular surface of a molecule. The molecular surface resembles the van der Waals surface of a molecule, except that crevices between atoms are smoothed over and interstices too small to accommodate the probe are eliminated. The surface includes cavities in the interior of the molecule, even if they are not accessible to a solvent molecule coming from the outside.

The molecular surface calculated is that defined by Richards (see the reference below). In particular, the calculated molecular surface is that traced out by the surface of the probe sphere rather that the probe sphere's center. According to Richards' definition, the molecular surface consists of two parts: contact surface and reentrant surface. The contact surface is made up of "those parts of the molecular van der Waals surface that can actually be in contact with the surface of the probe." The reentrant surface is defined by "the interior-facing part of the probe when it is simultaneously in contact with more than one atom." Dms reports the amounts of contact and reentrant surface area, and the combined total surface area on the standard error output (see -g).

Pdbfile is an input file of coordinates. The input file must be in the Protein Data Bank format. The first part of each atom name is used to determine the element type. By default, implicit hydrogens are included for carbon, nitrogen and oxygen atoms; thus, aromatic carbons and nitrogens will have van der Waals radii that are somewhat too big. Note that only amino acid and nucleic acid residues will be included unless -a is also specified.


Include all atoms, not just those in amino acid and nucleic acid residues.
-d density
Density is a factor affecting the density of points on the surface; the default of 1.0 produces about 5 points per square angstrom. Only values between 0.1 and 10.0 are permitted. A density of 0.5 is recommended for large molecules.
-g logfile
Write all the informative messages to logfile instead of the standard error output. Genuine errors still go to the standard error output. New log information is appended to logfile rather than overwriting it, and thus messages from several runs may be accumulated.
-i sitefile
Calculate the molecular surface only for those residues and atoms specified in sitefile, keeping the rest of the molecule for collision checks. Sitefile consists of lines such as the following:
ASP 205 CA
TYR 13 *
HIS 178 TO
The asterisk, *, means all atoms of the residue, and the "FRM" and "TO" lines mean all residues from 116 to 178 inclusive. The sequence number may contain letters, and if the PDB input file contains chain identifiers, then those should be appended on the right of the sequence number. Residue insertion codes (if any) should be placed between the sequence number and any chain identifier. Residues contained in HETATM records should have an asterisk appended to the end of the residue identifier. The surface generated using -i is not always the same as the surface generated by running the entire molecule and afterwards selecting the desired atoms. The first surface will not include reentrant surface lying between an atom in sitefile and atoms not in the file.
Include the unit normals to the surface with each surface point record.
-w radius
Change the "water" probe radius from the default of 1.4 angstroms. Radius must be between 1.0 and 201.0.
Produce more verbose output. Dms will announce each computation phase as it is entered as well as a count of the atom types in the molecule and the number of computation requests handled by each host that participated in the calculation.
-o outfile
The output surface is written to outfile. This flag is not optional.

The output consists of a series of atom and surface point records, with the same format for the first six fields. Each atom is followed by the surface points (if any) which belong to it. These first six fields are in the following format: residue name, sequence number, atom name, x coordinate, y coordinate, z coordinate. For an atom record, the seventh field is "A." For a surface point record, the seventh field begins with an "S," followed by a "C," "R," or "S" according to whether the point is part of contact, reentrant, or saddle surface (saddle is a type of reentrant surface where the probe is in contact with exactly two atoms). This is followed a digit used for depicting different density levels. The eighth field is the molecular surface area associated with the point in square angstroms. If -n is specified, the next three fields are the unit normal vector pointing outward from the surface. Messages and errors are written to the standard error output unless a separate log file has been specified with -g.

Dms reads the elements and radii from a file named radii. The default file is /usr/local/chimera/share/dms/radii. If there is a file in the current directory called radii, then dms will use that file instead. To add uncommon elements or use different radii, one should copy the default file and modify it. The file format is documented in the file itself.


Richards, F.M., "Areas, volumes, packing and protein structure," Ann. Rev. Biophys. Bioeng. 6, 151-176 (1977).


Conrad Huang
University of California, San Francisco


/usr/local/chimera/share/dms/radii - default atomic radii


Many and varied. Be sure to examine the output messages (standard error or logfile, if specified) before leaving a background job running.