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). ############################################################################ ## LICENSE: ############################################################################ 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 ############################################################################ ## REPORTING PROBLEMS AND ASKING QUESTIONS ############################################################################ 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 ############################################################################ ## INSTALLATION: ############################################################################ 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. ############################################################################ ## TEST ############################################################################ 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 ############################################################################ ## converting PDB to xyzr ############################################################################ 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 ############################################################################ ## REFERENCES: ############################################################################ (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/). ############################################################################ ## LICENSE ############################################################################ 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. ############################################################################ ## HOW TO CONTACT ME ############################################################################ 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