MSMS man page

MSMS(1) User Commands MSMS(1)

NAME

     msms

SYNOPSIS

 

msms [ -if filename ] [ -of filename ] [ -af filename ][ -probe_radius radius ] [ -density density ] [ -no_area ][ -surface <tses,ases> ] [ -socket servicename ] [ -sinetd ][ -noh ] [ -no_rest_on_pbr ] [ -no_rest ] [ -free_vertices ][ -all_components ] [ -one_cavity #atoms at1 [at2] [at3] ][ -no_header ]

DESCRIPTION

MSMS computes, for a given set of spheres S and a probe
radius rp , the Reduced Surface and the analytical model of
the Solvent Excluded Surface ( SES ). The SES can then be
triangulated with a given vertex density.The program can run in standalone or server mode – if
filename ). In server mode, the only requested option is the
socket name to be used to communicate with the client appli
cation ( -socket servicename or -sinetd ).

OPTIONS

Options may appear in any order and may be abbreviated. If
the abbreviation matches several options, the first match
will be used.

-if filename

Allows to specify the file from which the sphere set S
will be read. This file contains the center ( x,y,z )
and the radius r of one sphere per line. These number
are stored in a free format. Lines starting with the
character `#’ are treated as comments and are skipped.
This option is the only requested option when MSMS is
run in standalone mode. 

-of filename

 

Allows to specify the files in which to store the tri
angulated solvent excluded surface resulting from a
calculation. Two files will be created, one for ver
tices and one for faces. If the component number is 0,
files called filename.vert and filename.face are
created. For other components, the component number is
inserted in the file name, for example for the com
ponent number 3 the files are called filename_3.vert
and filename_3.face.
The face file contains three header lines followed by
one triangle per line. The first header line provides a
comment and the file name of the sphere set. The second
header line holds comments about the content of the
third line. The third header line provides the number
of triangles, the number of spheres in the set, the
triangulation density and the probe sphere radius. The
first three numbers are (1 based) vertex indices. The
next field can be: 1 for a triangle in a toric reen
trant face, 2 for a triangle in a spheric reentrant
face and 3 for a triangle in a contact face. The last
number on the line is the (1 based) face number in the
analytical description of the solvent excluded surface.
These values are written in the following format “%6d
%6d %6d %2d %6d”.
The vertex file contains three header lines (similar to
the header in the .face file) followed by one vertex
per line and provides the coordinates (x,y,z) and the
normals (nx,ny,nz) followed by the number of the face
(in the analytical description of the solvent excluded
surface) to which the vertex belongs. The vertices of
the analytical surface have a value 0 in that field and
the vertices lying on edges of this surface have nega
tive values. The next field holds the (1 based) index
of the closest sphere. The next field is 1 for vertices
which belong to toric reentrant faces (including ver
tices of the analytical surface), 2 for vertices inside
reentrant faces and 3 for vertices inside contact
faces. These values are written in the following format
“%9.3f %9.3f %9.3f %9.3f %9.3f %9.3f %7d %7d %2d”. 

-af filename

 

Allows to specify the name of the file used to store
solvent excluded and solvent accessible surface areas.
The surface areas in each surface component are listed
for every atom. 

-no_header

 

By default a 3 lines header is written into the .face
and .vert files. This flags allows no to write out
these headers. 

-probe_radius radius

 

Used to modify the default value of the probe sphere
radius (1.5 Angstrom). No check is done on the validity
of the probe radius. MSMS will fail to compute the tri
angulation template sphere for radii that are too small
or too large. Values ranging from 0.5 to 10 should pose
no problem. 

-density density

 

Used to modify the default triangulation density (1.0
vertex/Angstrom^2). No test is done on the validity of
this parameter. Typical values are 1.0 for large
molecules (>1000 atoms) and 3.0 for smaller molecules.

-no_area

This option allows to turn off the surface area compu
tation.

-surface <tses,ases>

Used to specify which surface to calculate. At the
moment, the only choices are I. tses for triangulated
solvent excluded surface and ases for analytical sol
vent excluded surface. By default the surface is tri
angulated. This option is mainly used to avoid triangu
lation, for instance, when one is interested only in
surface areas. 

-socket servicename

 

When MSMS is started with this option, the program
enters the server mode and “listens” to the specified
Unix domain socket for clients requesting this service.
If a client program requests this service the connec
tion is established and MSMS expects to get the compu
tation parameters and the spheres from the client thru
this socket. Once the calculation is completed MSMS
will send the triangulated surface to the client over
this socket. This option doesn’t use a general way to
encode values (like xdr) and works only on a limited
set of architectures. 

-sinetd

 

This option is used to put MSMS in the server mode when
MSMS is started by the internet daemon. This allows
MSMS to be started whenever a client program requests
MSMS to run. 

-noh

 

Used to skip atoms with radius 1.2…???? (I know !) 

-no_rest_on_pbr

 

Because of badly handled singular cases or numerical
instability, it can happen that MSMS has problems tri
angulating the surface. By default, the program will
restart the computation up to five times, after
increasing the radius of the atoms causing the problem
by 0.1 Angstrom. This option prevents MSMS from res
tarting the calculation if problems occur during the
triangulation of spherical reentrant faces (which often
points to singularities problems). The resulting tri
angulated surface won’t be correct and might have holes
(see also -no_rest). 

-no_rest

 

This option is used to prevent MSMS from restarting the
computation in any case (see also -no_rest_on_pbr). 

-free_vertices

 

By default, free vertices of the reduced surface are
not searched for. Use this option to force their detec
tion. 

-all_components

 

By default, only the external component of the molecu
lar surfaces (reduced and solvent excluded) are com
puted. This option allows to force MSMS to find all
components. If the -of filename option is specified,
files with extension .vert and .face will be created
for each component. 

-one_cavity #atoms at1 [at2] [at3]

 

With this option one can compute a specific component
of the molecular surfaces by indicating 1, 2 or 3
atom(s) the probe should initially touch. The number of
such atoms is specified in followed by the correspond
ing number of (0 based) atom indices.

EXAMPLE

Triangulate the solvent excluded surface of a set of spheres
and saving the triangulation in myset.vert and myset.face :

msms -if myset.xyzr -of myset

Compute all components of the surfaces for a probe radius of
1.4 and triangulate them with a density of 3.0:

msms -if myset.xyzr -de 3.0 -prob 1.4 -of myset

FILES

pdb_to_xyzr(1),

BUGS

If all the vertices of a component of the reduced surface
also belong to another component, MSMS fails to find this
component. A work around is to specify the first face for
that component explicitly using the -one_cavity option. 

The genus of the reduced surface is sometimes wrong.

 

 

Singular edges forming a full circles are not treated.

 

 

Normal vectors of singular vertices point arbitrarily to the
center of one of the probe they belong to.

 

 

MSMS will crash or produce weird results if a sphere of S is
entierly inside another sphere of S

 

AUTHOR

Michel F. Sanner,The Scripps Research Institute, La Jolla, California.

Last Modified: 04:04pm PST, February 05, 1996