MSMS man page

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    MSMS(1)                   User Commands                   MSMS(1)

## NAME

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         msms v2.5

## 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. Empty lines and Lines starting with the character `#' are treated as comments and are skipped. The radius can be followed by an optional atom name (string). This name, if present, will be appended to the vertices in the surface and area output files (see the new pdb_to_xyzrn script that adds atom names from pdb file). 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. Finally, if atom names were present in the input file, the name of the closest atom is written for each vertex. These values are written in the following format ``%9.3f %9.3f %9.3f %9.3f %9.3f %9.3f %7d %7d %2d %s''.

-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