Old software manuals

We present here a small collection of manuals for early crystallographic programs, for which we do not have copies of the source code. See also the Software Museum for several program packages where the source code is available.

• AXDA - ANDA (85 pages; numbered page 44 absent - not known whether missing or incorrect numbering)
  • AXDA - ANDA USERS INFORMATION MANUAL; A. L. Bednowitz, Brookhaven National Laboratory; Writeup modified by W. C. Hamilton, February 1969
    Automatic X-ray Data Acquisition and Automatic Neutron Data Acquisition
    AXDA and ANDA are programs written for X-ray and Neutron data acquisition with the BNL Multiple Spectrometer Control System. The basic programs provide the necessary computations for the startup and continuation of a data acquisition run. These programs provide for obtaining data in one of several modes of operation as desired by the experimenter. They have been designed to operate four-circle single crystal diffractometers. But, with small modifications they have also been applied to three-circle and even two-circle diffractometers.
  High resolution (42 MB) Low resolution (3.0 MB)
• FRODO (48 pages)
  • FRODO User's Guide; Stuart Oatley, University of California, San Diego; Original program: Alwyn Jones, University of Uppsala. November 1985
    A model building and refinement system is described for use with a Vector General 3400 graphical display. The system allows the user to build models using guide atoms and angles to arrive at the final conformation. It has been used to assist in difference Fourier map interpretation at medium and high resolution, and to build a protein molecule into a multiple isomorphous replacement phased electron density map.
  High resolution (34 MB) Low resolution (2.43 MB)
• MBLD (45 pages)
  • MBLD; M. S. Gordon and J. A. Pople, mid 1970s
    This program, from a minimal amount of input, builds a standardized geometric model of a molecule, and using standard values of bondlengths, angles, and dihedral angles implicit in the program, calculates the cartesian coordinates of all atoms in the molecule. In addition, options are available which allow the user to choose his own geometric parameters.
  High resolution (27 MB) Low resolution (2.1 MB)
• ORFFE (91 pages)
  • OR FFE, A FORTRAN crystallographic function and error program; W. R. Busing, K. O. Martin and H. A. Levy; ORNL-TM-305, March 1964
    A computer program that calculates interatomic distances, bond angles, principal axes of thermal motion, and other functions of the unit cell parameters, the atomic coordinates, and the temperature factor coefficients of a crystal structure is described. The standard errors of these functions are computed from the variance-covariance matrix of the parameters if this is known. The program may be used independently, or the input may be taken from a magnetic tape prepared by the crystallographic least-squares program OR FLS. The program is written entirely in Fortran, and detailed instructions for its use are included.
  Download (6.5 MB)  OSTI web site
• ORFLS (83 pages)
  • OR FLS, A FORTRAN crystallographic least-squares program; W. R. Busing, K. O. Martin and H. A. Levy; ORNL-TM-305, August 1962
    A computer program to perform the least-squares refinement of crystal structure parameters based on X-ray or neutron-diffraction measurements is described. The program is written mostly in the Fortran language to facilitate modification and to permit its use on various machines. Detailed instructions for its use are included, and the required card decks may be obtained.
  Download (5.7 MB)  OSTI web site
• ORTEP-II (130 pages)
  • OR TEP-II: A FORTRAN Thermal-Ellipsoid Plot Program for Crystal Structure Illustrations; Carroll K. Johnson; ORNL-5138, March 1976
    ORTEP2 draws crystal structure illustrations using a CalComp plotter. Ball and stick type illustrations of publication quality are produced with either spheres or thermal motion probability ellipsoids on the atomic sites. The program can produce stereoscopic pairs of illustrations which aid in the visualization of complex packing arrangements of atoms and thermal motion patterns. Interatomic distances, bond angles, and principal axes of thermal motion are calculated also as part of the structural study. ORTEP2 includes a hidden line algorithm to eliminate those portions of atoms or bonds behind other atoms or bonds.
  Download (4.0 MB)  OSTI web site
• ORTEP-III (180 pages)
  • ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations; Michael N. Burnett and Carroll K. Johnson; ORNL-6895, July 1996
    This report describes a computer program for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids on the atomic sites. The program can also produce stereoscopic pairs of illustrations which aid in the visualization of complex packing arrangements of atoms and thermal motion patterns. Interatomic distances, bond angles, and principal axes of thermal motion are also calculated to aid the structural study.
  Download (9.5 MB)  OSTI web site
• UCSD-MMS (44 pages)
  • The UCSD Molecular Modelling System Reference Manual; Steve Dempsey, Department of Chemistry Computer Facility, Department of Chemistry B-014, University of California, San Diego, La Jolla, CA 92093; 12 February 1986
    The UCSD Molecular Modelling System (MMS) is a collection of software tools that allow the user to view and interact with dynamic computer generated line drawing displays of molecular structures. This manual contains detailed descriptions of all of the commands and options available in the MMS.
  High resolution (29 MB) Low resolution (2.25 MB)
• UCSF MidasPlus (120 pages)
  • UCSF MidasPlus Molecular Interactive Display and Simulation User's Manual; Computer Graphics Laboratory, School of Pharmacy, University of California, San Francisco; May 1991
    The Molecular Interactive Display and Simulation (MIDAS) System is a collection of programs developed by the Computer Graphics Laboratory at the University of California, San Francisco. The major component of the MIDAS system is an interactive graphics display program, MidasPlus, designed for the display and manipulation of macromolecules such as proteins and nucleic acids. Several ancillary programs are also part of the system and allow for such features as computing the surface of a molecule, the selection of an active site region within a molecule, computation of electrostatic charge potentials, etc. At the core of MIDAS is an unusually coherent hierarchical database system, designed specifically for macromolecules and both compact in its storage requirements and fast in its data access.
  High resolution (109 MB) Low resolution (7.5 MB)
• X-RAY 67 (181 pages)
  • X-RAY 67 Program system for X-ray Crystallography; for the Univac 1108, CDC 3600/6600, IBM 360/50,65,75, IBM 7094; University of Maryland Technical Report 67-58; December 1967
    The X-RAY System of 1967 is a rewrite of X-RAY-63. It consists of a set of FORTRAN programs all interrelated and sharing mutual data files and data card formats. The programs are structured in two main divisions. The nucleus set (which is identified by the prefix NUC) and the working diffraction calculation set (which is identified by the prefix XY). The nucleus of the system has, in actuality, nothing to do with diffraction calculations, per se, but is rather an essentially FORTRAN sub-system monitor which allows any other FORTRAN program to be integrated into its librarv. The coding for all the X-RAY system has been done in a "neutral" FORTRAN IV and FORTRAN 66 "pidgen" dialect. NUC901 (NUSF) is able to translate the symbolic decks to take care of any individual peculiarities of the IBM 7094, UNIVAC 1107,1108, CDC 3600, CDC 6400, 6600, and the larger IBM 360 series. In addition to the care exercised in assuring the universality of the FORTRAN used, all of the local computer laboratory file numbers, page length, file commands, etc. are coded into carefully marked subroutines of the nucleus. Therefore changes in the diffraction programs are, as far as is known from experience on a few of the above named machines, eliminated.
  High resolution (142 MB) Low resolution (11 MB)