Installation of the ELLIPS Programs and Support Fortran Software: --------------------------------------------------------------------------- Introduction. The ELLIPS Programms (ELLIPS1, ELLIPS2, ELLIPS3, ELLIPS4) are a suite of four programs written for PC (486 or higher) for ellipsoidal representations of macromolecular shape in solution for quasi-rigid particles based on hydrodynamic measurement of "Universal" shape functions which are derived from the sedimentation coefficient, intrinsic viscosity, radius of gyration, molecular covolume and rotational hydrodynamic/ relaxation functions (from electro-optic decay, fluorescence anisotropy depolarisation decay or NMR). A full description of the Universal shape functions and the 4 programs are found in: Harding SE, Horton JC, Coelfen H (1997) The ELLIPS suite of macromolecular conformation algorithms, Eur. Biophys. J. 25: 347-359, and this paper MUST be consulted before use of the programs are attempted. This paper also describes how the Universal shape functions can be calculated from the experimental hydrodynamic parameters. [The hydrodynamic theory behind the calculation of the shape functions is exact.However, for those (quasi-rigid) macromolecules which cannot be reasonably represented by ellipsoids, the user is advised to use instead the Program SOLPRO, described in J. Garcia de la Torre, B. Carrasco-Gomez and S.E. Harding (1997) Eur. Biophys. J. 25, 361-372, which is based on modelling the particle as, and approximating the hydrodynamics by, a multi- array of spherical beads. The ELLIPS and SOLPRO programmes are designed to be entirely complementary] ELLIPS1: QUICKBASIC algorithm based on a simple ellipsoid of revolution model. It predicts the axial ratio (a/b) of the equivalent prolate or oblate ellipsoid of revolution from a user specified shape function ELLIPS2: FORTRAN77 algorithm based on general triaxial ellipsoid model. Evaluates the values of all the hydrodynamic shape functions from user specified values for the semi-axial dimensions (a,b,c) of a macromolecule or the axial ratios (a/b, b/c). [Works also for ellipsoids of revolution, just set c=b or b/c = 1 for a prolate ellipsoid, or c=a or a/b = 1 for an oblate ellipsoid. It can also be linked to a programme (ELLIPSE) written for the prediction of the (a,b,c) from a crystallographic structure [Taylor WR, Thornton JM, Turnell WG (1983) An ellipsoidal approximation of protein shape, J. Mol. Graphics 1, 30-38] ELLIPS3: FORTRAN77 algorithm based on general triaxial ellipsoid model. Evaluates the molecular shape (a/b, b/c) from combinations of hydration independent shape functions (2 versions: ELLIPS3s sends output to the screen, ELLIPS3p to a file which can be printed on a Dolby-Postscript compatible printer) ELLIPS4: FORTRAN77 algorithm based on general triaxial ellipsoid model. Evaluates the molecular shape (a/b, b/c) from electro-optic decay parameters combined with other hydrodynamic data. ----------------------------------------------------------------------------- Hardware requirement. 486 or higher PC For ELLIPS3p a Dolby Postscript compatible printer is required ----------------------------------------------------------------------------- Installation. 2 disks are supplied: DISK 1 contains the ELLIPS1-4 prorammes in a compressed form ("ELLIPS") and a README.TXT file (this printout here) DISK 2 contains the support software (Salford FORTRAN77) required for the running of ELLIPS2-ELLIPS4. ELLIPS1 can be run directly without this. 1. Create a directory on your C: drive - ELLIPS 2. Insert Disk1 into your A: drive. 3. Copy the contents across to the ELLIPS directory 4. Expand the file ELLIPS by double clicking on it if you are in File Manager or by typing its name if you are in DOS 5. Remove Disk1 6. Insert Disk2 into your A:drive. DO NOT COPY THE CONTENTS OF THIS DISK INTO YOUR C: DRIVE. If you do the installation procedure will fail. 7. Go into the A:drive directory 8. Double click the file INSTALL.EXE if you are in Windows or type INSTALL if you are in DOS. You will be confronted with a series of prompts: Welcome to Dbos... do you wish Y This is a 32 bit .... Y By default.. c:\DBOS.DIR ENTER (Carriage return) If you wish to use DBOS within windows 3... N Do you want me to add the products to AUTOEXEC.BAT Y Do you want DBOS to run each time you reboot N 9. Screen responds: dbos successfully installed..... and then returns to the dos prompt if you are in DOS or the file manager if you are in windows You are now ready to run the programmes. To do so, you just type ELLIPS1 for ELLIPS1. For ELLIPS2, ELLIPS3s, ELLIPS3p and ELLIPS4 you need to leave Windows and go in to DOS. Then type DBOS, and then press carriage return Then type run77 ELLIPS2 or run77 ELLIPS3s or run77 ELLIPS3p run77 ELLIPS4 When you have finished, and you wish to return to WINDOWS you will probably need to kill the DBOS command by typing kill_dbos. --------------------------------------------------------------------------- Input/Output formats ELLIPS1: input is at run-time. Screen only output. Screen dump for hard copy ELLIPS2: input is at run-time. Output is to the file output_2.txt ELLIPS3s: input is at run-time. Screen only output. ELLIPS3p: input is at run-time Output is to file PPPP3.cmd (To print this out the printer has to be Dolby Postscript compatible) ELLIPS4: input decay data as a user-named file input constraining hydrodynamic function data points either at run- time or as a user-named file output data as a user-named file WHEN RUNNING ALL PROGRAMS YOU SHOULD CONSULT THE EUR. BIOPHYS.J. 25, 347-359 (1997) REFERENCE VERY CLOSELY. Any problems contact me S.E. Harding 19/12/97 Steve.Harding@Nottingham.ac.uk