MSMS license

File contents

MSMS v2.5.7 (Michel F. SANNER Jan. 2006)

MSMS computes, for a given probe radius, the reduced surface of a set of
spheres. An analytical description of the solvent excluded surface is
computed from the reduced surface. Special attention is paid to the proper
handling of self-intersecting parts of the surface called singularities.
This analytical model of the solvent excluded surface can be triangulated
with a user specified vertex density (see references for more information).

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## LICENSE:
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In a nutshell:  
     - MSMS is free for academic use, for commercial use please contact me. 
    (sanner@scripps.edu)
     
    - Acknowledge the use of MSMS in any publication by citing:
    Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) Reduced surface:
    an efficient way to compute molecular surfaces. Biopolymers, Vol. 38.,
    (3), 305-320.

The full license text is at he end of this file

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## REPORTING PROBLEMS AND ASKING QUESTIONS
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Please send questions and report bugs to the msms mailing list:
	msms@scripps.edu

You can subscribe to this list at (very low traffic):
	http://mgldev.scripps.edu/mailman/listinfo/msms

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## INSTALLATION:
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if you read this file, you already un-tar'ed the file and you got the 
following files:

  - 1crn.pdb  	     : example of PDB file
  - README           : this file
  - atmtypenumbers   : data file used by the pdb_to_xyzr script 
  - msms.1           : unix man page for MSMS. Also available on the WWW
	 http://www.scripps.edu/sanner/html/msms_man.html
  - msms.html        : HTML version of the man page for MSMS.
  - msms."arch"      : Binary version of MSMS compiled for "arch".
  - pdb_to_xyzr      : Script to convert get XYZR coordinates from a PDB file.
  - pdb_to_xyzrn     : Script to convert get XYZRN coordinates from a PDB file.
  - 1crn.xyzr        : Example of XYZR atomic coordinates.
  - 1crn.xyzrn       : Example of XYZRN atomic coordinates.


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## TEST
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TEST MSMS:
	To test the program type:

	> ./msms."arch" -if 1crn.xyzr

this is the output:

MSMS 2.5 started on noah
Copyright M.F. Sanner (1994)
Compilation flags -Ofast -xansi -DVERBOSE -DTIMING -DFUNCPROTO -fullwarn
INPUT  ./1crn.xyzr 327 spheres 0 collision only, radii  1.400 to  2.000
PARAM  Probe_radius  1.500 density  1.000
REDUCED SURFACE ...
    RS component 0 identified 211 208 210
    0 free edge(s) found in component 0
    RS component  #faces  #edges #free_edges  #vertices   genus
         0         430      645          0        210      3.5
    Time Reduced Surface real: 0.20 user: 0.07 sys: 0.00
ANALYTICAL SOLVENT EXCLUDED SURFACE...
    Component   0
    25 probe capable to generate singularities
        Time Surface real: 0.08 user: 0.01 sys: 0.01
   SRDF...
 0 double edges removed
        Time Singularities real: 0.00 user: 0.01 sys: 0.00
    SES comp.  #fac.  #edg. #s_edg. #vert. #s_vert. R_h C_h genus
         0     1304   2616     12    1314       24   0   0    0
ANALYTICAL SURFACE AREA :
    Comp. probe_radius,   reent,    toric,   contact    SES       SAS
      0       1.500     487.240   907.580   927.972  2322.791  3054.258
TRIANGULATION...
    Component 0
    #components, vertices, edges, face, genus, density:      1   2465   7389   4926 0  1.061
        Time Triangulation real: 0.12 user: 0.05 sys: 0.00
NUMERICAL VOLUMES AND AREA
    Comp. probe_radius SES_volume SES_area)
       0      1.50     5131.227   2222.982
    Total ses_volume:  5131.227
MSMS terminated normally
Total Time real: 0.47 user: 0.15 sys: 0.02


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## converting PDB to xyzr
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ABOUT PDB_TO_XYZR:

  This c-shell script was written by Mike Pique (The Scripps Research
Institute) to get XYZR atomic coordinates from a Brookhaven Protein Data
Bank file (.pdb).
  It extract x,y,z from PDB file, generate radius of each atom Hydrogens
are presumed to be missing ("united atom" approach) in this version.

input: pdb file as argument or stdin
output: new xyzr file to stdout

examples:

   pdb_to_xyzr 1crn.pdb > 1crn.xyzr


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## REFERENCES:
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(1) Michel F. Sanner, Arthur J. Olson, Jean-Claude Spehner.(1996) Reduced
Surface: an efficient way to compute molecule surfaces. Biopolymers. Vol. 38.

(2) Michel F. Sanner, Arthur J. Olson, Jean-Claude Spehner. Fast and Robust
Computation of Molecular Surfaces. (1995) ACM 11th Symp. Comp. Geom. 
Vancouver B.C. Canada. C6-C7. (PostScript version available on the net
http://www.scripps.edu/pub/olson-web/people/sanner/).


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## LICENSE
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THIS IS WHAT YOU AGREED TO BY DOWNLOADING THE SOFTWARE:

1) The program (MSMS) received by you will be used only for scientific
   research. This license is issued to you as an individual. For institution
   wide use of the software you will have to follow the official registration
   procedure. To do so you can contact us by e-mail (olson@scripps.edu), mail
   (TSRI, Molecular Biology Department, TPC 26, 10550 North Torrey Pines Road,
   92037 La Jolla) or fax (858)-784-2860.

2. WE REQUEST THAT YOU AGREE TO ACKNOWLEDGE THE USE OF THE MSMS SOFTWARE THAT
   RESULTS IN ANY PUBLISHED WORK, INCLUDING SCIENTIFIC PAPERS, FILMS AND
   VIDEOTAPES BY CITING THE FOLLOWING REFERENCE:

    Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) Reduced surface:
    an efficient way to compute molecular surfaces. Biopolymers, Vol. 38.,
    (3), 305-320.

3. You will not sell or otherwise transfer these programs or derivatives to
   any other party, whether with or without consideration, for any purpose.

4. You will not obtain, and will not attempt to obtain copyright coverage
   thereon without the express purpose written consent of The Scripps Research
   Institute.

5. You will hold harmless from all or any expenses you may incur as a result
   of or arising from your use, direct or indirect, of these materials.  You
   understand that no other right or license to this program or its derivatives
   is granted or implied as a result of our transmission of same to you.


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## HOW TO CONTACT ME
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The prefered way to get information, ask questions, or find answers is
to use the (searchable) mailing list 
	msms@scripps.edu
	http://mgldev.scripps.edu/mailman/listinfo/msms

Mail:	Michel F. Sanner
	The Scripps Research Institute, TPC 26
	10550 North Torrey Pines Road, 92037 La Jolla
	CA-92037 USA

E-mail:	sanner@scripps.edu
WWW:	http://www.scripps.edu/~sanner

Tel.:	(858) 784-2341
Fax.:	(858) 784-2860