DMS(1)

NAME

dms - calculate a solvent-accessible molecular surface

SYNOPSIS

dms file [ -a ] [ -d density] [ -g file] [ -i file] [-n] [-w

radius] [-v] -o file

DESCRIPTION

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 F. M. Richards (1977, Ann. Rev. Biophys. Bioeng. ). 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 the -g flag below).

File is an input file of coordinates. The input file must be in the Protein Data Bank format. The first letter or first two letters of the 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.

Dms can be set up to run on multiple machines simultaneously for increased performance. By default, it only runs on the local host. The UCSF MidasPlus Installation Guide that came with the MidasPlus CD-ROM contains instructions on how to configure dms to use multiple machines.

If it is desired to simply visualize a small molecular surface from within MIDAS, it may be easier to use the makems(1) delegate, rather than run dms directly. Consult the makems manual page for further details.

OPTIONS

The flags may be in any order. The meanings of the flags are described below:

-a

Include all atoms, not just those in amino acid and nucleic acid residues.

-d

Change the density of points on the surface. 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. For large proteins, a density of 0.5 is recommended.

-g

Write all the informative messages to file, instead of the standard error output. Genuine errors still go to the standard error output. This file is not rewound at any time, so messages from several runs may be accumulated.

-i

Calculate the molecular surface only for those residues and atoms specified in file, but keeping the rest of the molecule for collision checks. The file consists of a series of lines such as the following: ASP 205 CA TYR 13 * GLY 116 FRM HIS 178 TO

The asterisk means all atoms of the residue and the ``FRM'' and ``TO'' 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 the -i flag is not always the same as the surface generated by running the entire molecule and afterwards selecting out the desired atoms. The first surface will not include reentrant surface lying between an atom in the -i file and atoms not in the file. The pdb2site(1) utility may be useful for generating site files. Consult the pdb2site manual page for further details.

-n

Include the unit normals to the surface with each surface point record.

-v

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 dms calculation.

-o

The output is written to file. This flag is not optional.

-w

Change the water probe radius from the default radius of 1.4 angstroms. This parameter must be between 1.0 and 201.0.

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 the -n flag is specified, the next three fields are the unit normal vector pointing outward from the surface. Informative messages and errors are written to the standard error output unless a -g file is specified.

The chemical elements and radii that the program handles are detailed in the table below. The program gets these values from the file /usr/local/midas/resource/dms/radii. If there is a file in the current directory called radii, then dms will use that file instead. So in order 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.

               __________________
               |Element   Radius |
               | H         1.20  |
               | C         1.90  |
               | N         1.50  |
               | O         1.40  |
               | F         1.35  |
               | P         1.90  |
               | S         1.85  |
               | Cl        1.8   |
               | Fe        0.64  |
               | Cu        1.28  |
               | Zn        1.38  |
               | Br        1.95  |
               | I         2.15  |
               | Other     1.90  |
               |_________________|

SEE ALSO

pdb2site(1), The UCSF MidasPlus Installation Guide

AUTHOR

Conrad Huang

University of California, San Francisco

FILES

     /usr/local/midas/resource/dms/radii        default atomic
     radii

DIAGNOSTICS

Many and varied. Be sure to examine the -g file before you leave a background job running overnight.