Xtal3.0 INFORMATION ==================== Xtal3.0 is a portable software package for small molecule and macromolecular crystallographic calculations. A general description of the Xtal concepts is given by Hall, Stewart and Munn (1980) Acta Cryst. A36, 979-989. Xtal achieves portability through the use of the preprocessor language ratmac (which is related to ratfor). The ratmac precompiler converts the Xtal source code into fortran77. The preprocessor also provides a powerful 'macro editor' facility which enables machine-specific aspects of the source to be concentrated into a small library applicable to a wide range of computers. In this way Xtal achieves portability and machine efficiency. Xtal3.0 can be implemented at any computer with the following minimum specifications: 32-bit integer and real numbers; one Mb of RAM available to the user (or virtual memory); 30 Mb of disc storage; a Fortran77 compiler; and access to a 1600 bpi tape drive. A customised version is also available for use on PC computers with the following minimum specifications: IBM AT or compatable; 536 Kb memory available to the user; maths co-processor; MS-DOS or MS-OS/2; MS Fortran-77 Version 5.0; 20 Mb disc storage. Xtal3.0 Calculations --------------------- Xtal3.0 contains programs for 85 different crystallographic calculations. The function of these programs is given below. The Xtal System permits a sequence of calculations to be chained together in a single run. Data is automatically passed from program to program via an archive binary file. Most Xtal programs are general and may be applied to crystal structures of any size or symmetry. Others are intended for macromolecular calculations (these are flagged below with an asterisk *). For complete details of these programs read the Xtal3.0 Reference Manual. For your convenience the major calculations in the system are shown in bold. ABSCAL *applies phi-spin measured absorption corrections ABSORB apply Gaussian, analytical or spherical absorption corrections ADDATM load and check atom site parameters to the binary file ADDMUL *load XENGEN area detector data to the binary file ADDREF load and reduce reflection data to binary file APMASK *apply density solvent flattening mask ATABLE prepare table of atomic site parameters for publication BAYEST process intensity data using Bayesian statistics BFOURR *prepare special Fourier coefficients for FOURR BONDAT generate atom coordinates from molecular geometry BONDLA calculate molecular geometry lengths and angles CEDAR *atom refinement using energy, geometry & dynamics constraints CHARGE calculates the atomic charge from the electron density CIFIO reads and generates crystallographic Information File (CIF) CONTRS contour Fourier maps for graphical display CONVOL *generate Fourier coefficients for convolution map CRITIQ *determine the most variable reflections CRYLSQ refine atomic parameters by least-squares DIFDAT process diffractometer output data (CAD, Nicolet & others) EDTBDF edit the contents of the binary file FC calculate structure factors FINDKB *get scale & thermal displacement parameter for protein data FODIFF *map difference between two fourier maps FOGEN generate a map volume from an asymmetric unit map FOGNU *generate a map volume from a unit cell map FOSTAT *provide Fourier map density statistics FOURR map Beevers-Lipson and Fast Fourier Transform GENEV normalize structure factors GENSIN generate structure invariant relationships GENTAN estimate phases using generalized tangent procedures LATCON refine cell constants from measured two-thetas LISTFC list structure factor data for publication LSQPL calculate least squares planes MAKBRK *generate map data for FRODO input MAPLST convert FOURR map into list of densities (for Mathematica) MEDENS *maximum entropy phase refinement MEFFIT *restore F values after MEDENS run MERGDS *select data for addition or replacement MERGOB *merge data from two binary files MERUN *prepare control lines for MEDENS/MEFFIT runs MIR *apply multiple isomorphous refinement techniques MKMASK *make solvent density flattening mask MODEL search for molecular connections in Fourier map MODHKL modify reflection data on binary file MOGIN prepare atom coordinates for MOGLI input MULIST *list mult.-obs. reflection data NEWMAN calculate Newman projection data for selected atoms NICNAK process profile data on Nicolet diffractometer tape ORTEP calculate thermal ellipsoid data for plotting PARTN determines the contribution of an atom to the density map PATSEE find mole. fragment using Pat. map and structure invariants PEAKIN enter pseudo-peaks for processing by modelling software PEKPIK search for density max/min in Fourier map PERFAC estimate monochromator perfection factor from Irel's PHACMP compare phases of two sets of structure factors PHONYD generate phony data for testing statistics PIG interactive display and manipulation of molecular sites PLOT/PLOTX generate graphical outputs of ABSORB, CONTRS, NEWMAN, ORTEP PRECED *load atom data for CEDAR PROATM *loads protein atomic data in the Brookhaven database format PROLSQ *Konnert-Hendrickson restrained structure factor least squares PROTIN *Konnert-Hendrickson restraint builder REFM87 convert Xtal bdf to SCFS format and reverse REMSET *remove data set from multiple data set binary file REGFE calculate crystallographic functions and errors based on ORFEE REGWT calculates range of least squares weights REMSET *remove a complete data set from the bdf REVIEW review structure invariant phase relationship statistics RFOURR reverse Fourier transform. density -> structure factors RIGBOD transform atom parameters to a different unit cell RMAP map R-factors to find translated molecular fragment RSCAN scan structure factor agreement by R-factors SCALE1 *places independently measured data sets on same scale SHELIN input and execute standard Shelx lines to create Xtal bdf SIMPEL estimate phases using symbolic addition procedure SIMWGT *combine Sim weights with Hendrickson-Lattman coefficients SLANT interpolate slanted map from FOURR map SORTRF sort and merge reflection data on F, F**2 and I STARTX create binary data file and load symmetry and cell data VUBDF display the contents of any binary data file VUFILE display the contents of any line file Future Xtal Developments ------------------------ Additional programs are currently being developed for release in 1992. Xtal is a collaborative venture involving laboratories with a wide range of crystallographic interests. Our charges are used principally to distribute and maintain the system. Financing new software development is primary responsibility of program author(s). In this way development costs are borne by collaborating laboratories and agencies so that charges are kept as low as possible. Users are encouraged to contribute to the development of Xtal software. New software must meet the requirements laid down for Reference Manual and undergo testing at selected sites. The decision to distribute and support a new program is the responsibility of the Xtal Coordinator. A user wishing to develop software for general distribution should first contact the Coordinator to avoid unnecessary duplication with existing efforts. Xtal Implementation Support --------------------------- Detailed implementation instructions are supplied as part of the documentation. If a user requires additional assistance, either with implementation or subsequent applications, the following Xtal developers may be contacted. Asia: Syd Hall, Crystallography Centre, University of Western Australia, Nedlands 6009 AUSTRALIA phone:[619] 380-2725 email: syd@crystal.uwa.oz.au fax: [619] 380 1118 Europe: Geoff King, Kristallografi, University of Leuven, Celestijnenlaan 200c, B-3030 Heverlee, BELGIUM [32] 016-201015 fgeea01@blekul11.bitnet fax: [32] 016-201368 America: Jim Stewart, Department of Chemistry, University of Maryland, College Park, MD 20742, U.S.A. [1] 301-454-4623 jstew@umd2.umd.edu This support will normally be provided by fax or e-mail. However, if the implementor is able to underwrite the expenses, an effort will be made to visit the site. It must be emphasised, however, that the initial distribution charge implies no obligation to provide such a service. Xtal3.0 Purchase ---------------- Xtal3.0 is distributed by the Crystallography Centre at the University of Western Australia. To place an order for Xtal fill out the attached ORDER FORM and send with a purchase order or an international bank check (in US dollars) made payable to "XTAL, Crystallography, UWA", to: XTAL Coordinator, Crystallography, UWA, Nedlands 6009, Australia. Retain a copy of the order for future reference. An Xtal3.0 tape and documentation will be forwarded by air post within four weeks of receipt of this order. Initial Purchase A first-time purchasers of the system receive the Initial Distribution Package. This includes the tape (or floppies if the PC version is requested) containing source and implementation software; the Xtal3.0 documentation consisting of a Reference Manual and a Users Guide and a maintenance agreement covering the first two year period. The maintenance agreement provides for all software updates that are distributed during this period, plus periodic Newsletters. Maintenance Agreement The purchases of subsequent Xtal releases are handled within the Xtal maintenance agreement. If this is continued, users will automatically receive each new release of the system.This only applies if the maintenance does not lapse. Otherwise an order is treated as a first-time purchase. Standard and PC Versions Two versions of Xtal3.0 are available. The standard version supplied on magnetic tape may be implemented on any 32 bit computer. The PC version is customised for that application only. If both versions are ordered there is an additional charge of US$100. Academic and Industrial Users There is a price differential between academic and industrial users. Academic users are educational institutions or government laboratories. Users not in this category are classed as industrial users. Conditions of Purchase The supply of the Xtal System is conditional on the agreement that Xtal software and documentation be used solely at the site designated on the ORDER FORM. Neither the software nor documentation may be copied for any use whatsoever without the explicit written consent of the Xtal Coordinator. Copyright on Xtal software and documentation is reserved. Xtal3.0 Charges (in US dollars) [after Oct91] Academic Industrial Initial Distribution Package (1 year ) $1000 $2000 Maintenance Agreement 1992- (2 years) $ 500 $1000 Additional documentation Reference Manual $50 User's Guide $20 ----------------------------------------------------------------------------- Xtal3.0 Order Form ------------------- Distribution of Xtal3.0 started in September 1990. Complete the information below and accompany this sheet with a purchase order number or payment by an international bank check. All charges are in US dollars. Charges depend on whether you are an academic or an industrial user. If Xtal is to be used at an educational institution or a government research laboratory you are classed as an academic user. Otherwise you are classed as an industrial user. Academic Industrial Xtal3.0 Initial Distribution Package* $1000 $2000 $...... Maintenance Agreement* 1992 to 199... $ 500 /2yr. $1000 /2yr. $...... Additional documentation: Xtal3.0 Reference Manual $ 50 $...... Xtal3.0 User's Guide $ 20 $...... * Includes 1 Ref. Manual & 1 User's Guide US dollars TOTAL $...... System should be supplied for: [ ] standard computer [ ] PC [ ] both (add $100) For PC version give floppy size and density: [ ] 5.25" [ ] 3.5" [ ] High [ ] Double Future Xtal maintenance agreements to be renewed by autobilling: [ ] yes [ ] no Name of computer site where Xtal implemented ................................................................ Purchaser's Name and Address Purchase no..................... ..................................... Ph:..................... ..................................... Fx:..................... ..................................... Em:..................... ..................................... Declaration: I certify that the above items are to be purchased for installation and exclusive use at the above named computer site. Purchaser's Signature:..................... Dated:.../..../.... Send to: XTAL, Crystallography, UWA, Nedlands 6009, AUSTRALIA. or Fax: 619 380 1118 or Email: syd@crystal.uwa.oz.au