{"id":223,"date":"2019-03-08T00:08:47","date_gmt":"2019-03-08T00:08:47","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/msms\/?page_id=223"},"modified":"2019-10-17T23:13:43","modified_gmt":"2019-10-17T23:13:43","slug":"documentation","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/msms\/documentation\/","title":{"rendered":"Documentation"},"content":{"rendered":"

This page was last updated on October 17th, 2019 at 11:13 pm<\/p>

MSMS man page<\/h3>\n<\/div>
<\/div>
<\/div><\/div>
<\/div>
<\/div><\/div><\/div><\/div><\/div>

 <\/p>\n

MSMS(1) User Commands MSMS(1)<\/h3>\n

 <\/p>\n

NAME<\/h2>\n
     msms\r\n<\/pre>\n
\n
\n
SYNOPSIS<\/h2>\n
 <\/dt>\n
msms<\/b> [ -if<\/a> filename ] [ -of<\/a> filename ] [ -af<\/a> filename ][ -probe_radius<\/a> radius ] [ -density<\/a> density ] [ -no_area<\/a> ][ -surface<\/a> <tses,ases> ] [ -socket<\/a> servicename ] [ -sinetd<\/a> ][ -noh<\/a> ] [ -no_rest_on_pbr<\/a> ] [ -no_rest ] [ <\/a>-free_vertices<\/a> ][ <\/a>-all_components<\/a> ] [ <\/a>-one_cavity<\/a> #atoms at1 [at2] [at3] ][ <\/a>-no_header<\/a> ]
\n<\/a><\/dd>\n
\n
DESCRIPTION<\/h2>\n<\/dt>\n
MSMS computes, for a given set of spheres S and a probe
\nradius rp , the Reduced Surface and the analytical model of
\nthe Solvent Excluded Surface ( SES ). The SES can then be
\ntriangulated with a given vertex density.The program can run in standalone or server mode – if
\nfilename ). In server mode, the only requested option is the
\nsocket name to be used to communicate with the client appli
\ncation ( -socket servicename or -sinetd ).<\/dd>\n
\n
OPTIONS<\/h2>\n<\/dt>\n
Options may appear in any order and may be abbreviated. If
\nthe abbreviation matches several options, the first match
\nwill be used.<\/p>\n
\n
<\/a> -if filename <\/i><\/b><\/dt>\n
Allows to specify the file from which the sphere set S
\nwill be read. This file contains the center ( x,y,z )
\nand the radius r of one sphere per line. These number
\nare stored in a free format. Lines starting with the
\ncharacter `#’ are treated as comments and are skipped.
\nThis option is the only requested option when MSMS is
\nrun in standalone mode. <\/dd>\n
<\/a> -of filename <\/i><\/b><\/dt>\n
 <\/dd>\n
Allows to specify the files in which to store the tri
\nangulated solvent excluded surface resulting from a
\ncalculation. Two files will be created, one for ver
\ntices and one for faces. If the component number is 0,
\nfiles called filename.vert and filename.face are
\ncreated. For other components, the component number is
\ninserted in the file name, for example for the com
\nponent number 3 the files are called filename_3.vert
\nand filename_3.face.
\nThe face file contains three header lines followed by
\none triangle per line. The first header line provides a
\ncomment and the file name of the sphere set. The second
\nheader line holds comments about the content of the
\nthird line. The third header line provides the number
\nof triangles, the number of spheres in the set, the
\ntriangulation density and the probe sphere radius. The
\nfirst three numbers are (1 based) vertex indices. The
\nnext field can be: 1 for a triangle in a toric reen
\ntrant face, 2 for a triangle in a spheric reentrant
\nface and 3 for a triangle in a contact face. The last
\nnumber on the line is the (1 based) face number in the
\nanalytical description of the solvent excluded surface.
\nThese values are written in the following format “%6d
\n%6d %6d %2d %6d”.
\nThe vertex file contains three header lines (similar to
\nthe header in the .face file) followed by one vertex
\nper line and provides the coordinates (x,y,z) and the
\nnormals (nx,ny,nz) followed by the number of the face
\n(in the analytical description of the solvent excluded
\nsurface) to which the vertex belongs. The vertices of
\nthe analytical surface have a value 0 in that field and
\nthe vertices lying on edges of this surface have nega
\ntive values. The next field holds the (1 based) index
\nof the closest sphere. The next field is 1 for vertices
\nwhich belong to toric reentrant faces (including ver
\ntices of the analytical surface), 2 for vertices inside
\nreentrant faces and 3 for vertices inside contact
\nfaces. These values are written in the following format
\n“%9.3f %9.3f %9.3f %9.3f %9.3f %9.3f %7d %7d %2d”. <\/dd>\n
<\/a> -af filename<\/i><\/b><\/dt>\n
 <\/dd>\n
Allows to specify the name of the file used to store
\nsolvent excluded and solvent accessible surface areas.
\nThe surface areas in each surface component are listed
\nfor every atom. <\/dd>\n
<\/a> -no_header<\/i><\/b><\/dt>\n
 <\/dd>\n
By default a 3 lines header is written into the .face
\nand .vert files. This flags allows no to write out
\nthese headers. <\/dd>\n
<\/a> -probe_radius radius<\/i><\/b><\/dt>\n
 <\/dd>\n
Used to modify the default value of the probe sphere
\nradius (1.5 Angstrom). No check is done on the validity
\nof the probe radius. MSMS will fail to compute the tri
\nangulation template sphere for radii that are too small
\nor too large. Values ranging from 0.5 to 10 should pose
\nno problem. <\/dd>\n
<\/a> -density density<\/i><\/b><\/dt>\n
 <\/dd>\n
Used to modify the default triangulation density (1.0
\nvertex\/Angstrom^2). No test is done on the validity of
\nthis parameter. Typical values are 1.0 for large
\nmolecules (>1000 atoms) and 3.0 for smaller molecules.<\/dd>\n
<\/a> -no_area<\/i><\/b><\/dt>\n
This option allows to turn off the surface area compu
\ntation.<\/dd>\n
<\/a> -surface <tses,ases><\/i><\/b><\/dt>\n
Used to specify which surface to calculate. At the
\nmoment, the only choices are I. tses for triangulated
\nsolvent excluded surface and ases for analytical sol
\nvent excluded surface. By default the surface is tri
\nangulated. This option is mainly used to avoid triangu
\nlation, for instance, when one is interested only in
\nsurface areas. <\/dd>\n
<\/a> -socket servicename<\/i><\/b><\/dt>\n
 <\/dd>\n
When MSMS is started with this option, the program
\nenters the server mode and “listens” to the specified
\nUnix domain socket for clients requesting this service.
\nIf a client program requests this service the connec
\ntion is established and MSMS expects to get the compu
\ntation parameters and the spheres from the client thru
\nthis socket. Once the calculation is completed MSMS
\nwill send the triangulated surface to the client over
\nthis socket. This option doesn’t use a general way to
\nencode values (like xdr) and works only on a limited
\nset of architectures. <\/dd>\n
<\/a> -sinetd<\/i><\/b><\/dt>\n
 <\/dd>\n
This option is used to put MSMS in the server mode when
\nMSMS is started by the internet daemon. This allows
\nMSMS to be started whenever a client program requests
\nMSMS to run. <\/dd>\n
<\/a> -noh<\/i><\/b><\/dt>\n
 <\/dd>\n
Used to skip atoms with radius 1.2…???? (I know !) <\/dd>\n
<\/a> -no_rest_on_pbr<\/i><\/b><\/dt>\n
 <\/dd>\n
Because of badly handled singular cases or numerical
\ninstability, it can happen that MSMS has problems tri
\nangulating the surface. By default, the program will
\nrestart the computation up to five times, after
\nincreasing the radius of the atoms causing the problem
\nby 0.1 Angstrom. This option prevents MSMS from res
\ntarting the calculation if problems occur during the
\ntriangulation of spherical reentrant faces (which often
\npoints to singularities problems). The resulting tri
\nangulated surface won’t be correct and might have holes
\n(see also -no_rest). <\/dd>\n
<\/a> -no_rest<\/i><\/b><\/dt>\n
 <\/dd>\n
This option is used to prevent MSMS from restarting the
\ncomputation in any case (see also -no_rest_on_pbr). <\/dd>\n
<\/a> -free_vertices<\/i><\/b><\/dt>\n
 <\/dd>\n
By default, free vertices of the reduced surface are
\nnot searched for. Use this option to force their detec
\ntion. <\/dd>\n
<\/a> -all_components<\/i><\/b><\/dt>\n
 <\/dd>\n
By default, only the external component of the molecu
\nlar surfaces (reduced and solvent excluded) are com
\nputed. This option allows to force MSMS to find all
\ncomponents. If the -of filename option is specified,
\nfiles with extension .vert and .face will be created
\nfor each component. <\/dd>\n
<\/a> -one_cavity #atoms at1 [at2] [at3]<\/i><\/b><\/dt>\n
 <\/dd>\n
With this option one can compute a specific component
\nof the molecular surfaces by indicating 1, 2 or 3
\natom(s) the probe should initially touch. The number of
\nsuch atoms is specified in followed by the correspond
\ning number of (0 based) atom indices.<\/dd>\n<\/dl>\n<\/dt>\n<\/dl>\n
EXAMPLE<\/h2>\n
\n
Triangulate the solvent excluded surface of a set of spheres
\nand saving the triangulation in myset.vert and myset.face :<\/p>\n
\n
msms -if myset.xyzr -of myset<\/dd>\n<\/dl>\n<\/dd>\n
Compute all components of the surfaces for a probe radius of
\n1.4 and triangulate them with a density of 3.0:<\/p>\n
\n
msms -if myset.xyzr -de 3.0 -prob 1.4 -of myset<\/dd>\n<\/dl>\n<\/dd>\n<\/dl>\n
FILES<\/h2>\n
\n
pdb_to_xyzr(1),<\/dd>\n<\/dl>\n
BUGS<\/h2>\n
\n
If all the vertices of a component of the reduced surface
\nalso belong to another component, MSMS fails to find this
\ncomponent. A work around is to specify the first face for
\nthat component explicitly using the -one_cavity option. <\/dd>\n
The genus of the reduced surface is sometimes wrong.<\/dd>\n
 <\/p>\n
 <\/dd>\n
Singular edges forming a full circles are not treated.<\/dd>\n
 <\/p>\n
 <\/dd>\n
Normal vectors of singular vertices point arbitrarily to the
\ncenter of one of the probe they belong to.<\/dd>\n
 <\/p>\n
 <\/dd>\n
MSMS will crash or produce weird results if a sphere of S is
\nentierly inside another sphere of S<\/dd>\n
 <\/dd>\n<\/dl>\n
AUTHOR<\/h2>\n
Michel F. Sanner,The Scripps Research Institute, La Jolla, California.<\/p>\n
\n
Last Modified: 04:04pm PST, February 05, 1996<\/h5>\n<\/div>
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