Software


PROTEUM Crystallographic Software Suite


The PROTEUM suite is a collection of powerful software tools for macromolecular crystallography. The suite provides the highest quality results from date acquisition to reduction. The package is available for both Windows and Linux Redhat and includes:

  • Both Fourier (DENZO/DPS) and vector (SMART) indexing algorithms
  • A reciprocal lattice viewer that allows direct editing of harvested reflections
  • Cosmo: a novel data collection strategy tool
  • An innovative 3-D profile analysis and refinement engine for integration
  • SADABS for scaling and multi-scan absorption corrections
  • Integrated data base for easy analysis and secure, convenient archiving

The PROTEUM software has a completely new approach on how a user interacts with a crystallographic experiment. The Graphical User Interface guides the user through the complete experiment with minimal user input and maximal graphical feedback. The GUI lets the user focus on the experiment at hand and does not require any knowledge about instrument geometry or data collection strategies.

Run the experiment from the convenience of your office; PROTEUM features remote access capabilities allowing data collection to be setup and monitored from almost anywhere. The suite uses a server/client configuration to separate hardware control from the crystallographic experiment. The server computer is connected to the instrument and manages the system while the client connects through the local network and performs the higher level tasks.

PROTEUM is easy to use for the novice but has all the features required by expert crystallographers. Along with the user friendly GUI, intelligent defaults have been coded into the software to help streamline data collection. For those challenging problems, the suite has built-in functionality that will allow you to tackle anything from twinned crystals to SAD phasing.

XPREP

The propriety version of XPREP is now fully integrated into PROTEUM. Developed and maintained by Professor George Sheldrick at Goettingen University, XPREP is a versatile data analysis tool which features: space group determination, statistical evaluation of data, generation of anomalous dispersion files, Patterson map calculations and much more.

 


SHELX for Structural Biology

George Sheldrick, the author of the SHELX software for Crystal Structure Determination and Refinement, has written a number of programs to assist in solving problems in the field of Structural Biology.

XPREP

  • Available with PROTEUM software as well as standalone
  • Supported under Windows, LINUX, IRIX and MAC
  • Reciprocal space displays to check completeness of data
  • Processes MAD, SIR, SAD, SIRAS data
  • Checks for anomalous signal
  • Displays Harker sections of Patterson maps
  • Checks heavy atom derivative data
  • Displays self-rotation functions to search for non-crystallographic symmetry
  • Detect twinning

SHELXD

The structure solution program SHELXD is a powerful tool for locating the heavy atoms or anomalous scatterers from SIR, SAD, SIRAS or MAD data. Using Patterson methods and dual space recycling it will come up with a list of solutions. These solutions can be either viewed in a PDB viewer or fed into SHELXE.

SHELXE

The program following SHELXD uses the heavy atom information phasing and density modification to calculate electron density maps from the protein under investigation. For solvent flattening it used the sphere of influence method and solvent flipping. This often results in experimental electron density maps that hardly differ from maps that are obtained after refinement.

SHELXPRO

The program SHELXPRO has been added as an interactive user interface between SHELXL and other programs often used by protein crystallographers. It features:

  • Communication with other protein programs: Reading of hkl files, HKL2000 format conversion, R-free calculation, reading and writing and depositing pdb files
  • Creation of map (and pdb) files for various graphics packages (O, XtalView, Coot)
  • Analysis of a structure after refinement with SHELXL: Progress of LS refinement, Thermal displacement analysis, Ramachandran plot, Kleywegt NCS plot, NCS analysis, Reflection statistics, Luzzati plot, Esd analysis, Least-squares fit, Anisotropic scaling