Links to Crystallographic Web Sites


Crystallography Equipment

Crystallography Software

Data Processing, Structure Solution, and Refinement

  • AUSPEX Crystallographic data pathology analysis.
  • ARP/wARP Crystallographic model building and structure refinement.
  • Babel A program to convert a number of coordinates file formats
  • CCP4 CCP4 - Macromolecular Crystallography
  • CNS CNSsolve - Crystallography & NMR System
  • Crystals single crystal X-ray structure refinement and analysis
  • HIC-Up Hetero-compound Information Centre - Uppsala
  • HKL HKL package (Denzo, XDisplayF and Scalepack)
  • MOSFLM A program for integrating single crystal diffraction data
  • Oscail 9 Windows software for crystallography and molecular modeling
  • PMB A wrapper for CNS refinement & MORE!!!
  • PHENIX A complete structure refinement package: SOLVE/RESOLVE/TEXTAL/refine ...
  • Powder Diffraction Tools: Fit2D : d1Dplot : Dioptas : pyFAI : GSAS-II : FormagiX : Apex4$ : XRD2DScan$ : CrysAlis Pro$ :
  • PRODRG Create ligand topology files.(CCP4)
  • RAPPER Ensemble of models refinement.(CCP4)
  • SHARP Experimental phasing of macromolecular crystal structures
  • SHELX MAD/SIRAS and high resolution refinement.
  • SnB A Direct-Methods Procedure for Determining Crystal Structures
  • Solve Automated crystallographic structure solution for MIR and MAD (Phenix)
  • TLSMD TLS Motion Determination
  • Xtal System of Crystallographic Programs
  • XtalView Crystallographic software package for fitting electron density maps and solving structures by MIR and MAD
  • LAFIRE Automatic Model building

Molecular Graphics Interface

  • BobScript Robert Esnouf's extensions to MolScript version 1.4
  • Chimera UCSF Molecular Modeling
  • COOT Model Building GUI (LISP Guide)
  • PyMOL Molecular Graphics System
  • VMD Visual Molecular Dynamics
  • Dino Visualizing Structural Biology
  • Grasp Graphical Representation and Analysis of Structural Properties
  • MIfit The modern XFIT program for model building.
  • MolMol MOLecule analysis and MOLecule display
  • MolScript The Official Web Site
  • O WWW server Model-building etc.
  • Platon A Multipurpose Crystallographic Tool
  • RasMol Molecular Visualization
  • Raster3D Tools for generating high quality raster images of proteins or other molecules.
  • SPOCK A Full-Featured Molecular Graphics Program
  • SURFNET Visualizing molecular surfaces, cavities and intermolecular interactions
  • Swiss-PdbViewer A user friendly protein viewer for analysis and graphics

Structure Analysis

  • 3DNA Analyzing and rebuilding 3-dimensional nucleic acid structures
  • MOLPROBITY Analyzing protein structures

Frequently Asked Questions

  • XPLOR-FAQs
  • Software Lists for Crystallography

    • SINCRIS IUCr - Full Software List
    • PDB Software for structure determination and analysis
    • USF Uppsala Software Factory (Gerard J. Kleywegt)

    Software Lists for Chemistry


    Crystallization - Chemicals
    • BMCD Biological Macromolecule Crystallization Database
    • BDP / Xtalbase OpenEye's Biological Macromolecule Crystallization Database
    • Crystool Computing of a high efficiency screening protocol for crystals
    • Hampton Hampton Research
    • Millipore Tools, technologies and services for bioscience
    • Molecular Dimensions Products for biomolecular structure research
    • SIGMA-ALDRICH Sigma, Aldrich, Fluka, SUPELCO, ...

    Molecular Biology Resources
    • CMS MBR CCMS Molecular Biology Resource
    • DOCK Blaster Web-based DOCK interface
    • ENTREZ Life Science Search Engine
    • NCBI National Center for Biotechnology Information
    • WIKI Biology Encyclopedia
    • SER Surface Entropy Reduction
    • 3D-Jigsaw

    Computational Biology
    • HEX Hex is an interactive protein docking and molecular superposition program
    • DOCK Blaster Web-based DOCK interface
    • VINA AutoDock AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

    Synchrotron Facilities
    • Anomalous Scattering of Elements (Merritt)
    • ALS Advanced Light Source (Berkeley, CAL)
    • ALS-BCSB Berkeley Center for Structural Biology
    • APS Advanced Photon Source (Chicago, IL)
    • BIOSYNC Structural Biology Synchrotron Users Organization
    • CAMD PX1 Synchrotron Beamline (Baton Rouge, LA)
    • CHESS Cornell High Energy Synchrotron Source
    • ESRF European Synchrotron Radiation Facility
    • NSLS National Synchrotron Light Source (Brookhaven, NY)
    • SSRL Stanford Synchrotron Light Source (Menlo Park,CA)

    Data Bases
    • 3D EM 3-Dimensional Electron Microscopy
    • UBDB Aspherical Atom (University of Buffalo) Data Bank
    • CCDC Cambridge Crystallographic Data Centre
    • EM Data Bank Electron Microscopy Data Bank
    • Genbank Nucleotide Sequence Search
    • HAD Heavy Atom Databank
    • Ligand Depot Ligand PDB and CIF data (Rutgers)
    • MDB Metalloprotein Data Base and Browser
    • Tanna Metal Ion Coordination Database
    • NDB Nucleic Acid Database
    • PDB Protein Data Bank
    • PMP Protein Model Portal - Theoretical Models
    • PDBsum Summaries and structural analyses of PDB data files
    • PubMed Advanced MEDLINE Search
    • WebElements The periodic table on the WWW
    • X-ray Anomalous Scattering An introductory tutorial to anomalous scattering and a general tool for experiments based on anomalous scattering
    • ZINC A free database of commercially-available compounds for virtual screening

    Journals {MML} {ILLiad}

    IUCr's Crystallography World Wide
    • IUCr's CWW The IUCr's Crystallography World Wide
    • WDC The IUCr's World Database of Crystallographers

    HTML

    Visit our friends

    UTMB

    Public

    Basic Science Departments:
    Biochemistry & Molecular Biology
    Neuroscience & Cell Biology
    Pharmacology & Toxicology
    Microbiology & Immunology
    Sealy Centers & Institutes:
    Center for Structural Biology
    Center on Aging
    Center for Molecular Medicine
    Institute for Vaccine Science
    Institute for Drug Discovery

    SCSB

    Home

    Faculty
    Resources
    Facilities

    Publications
    Synposium
    Seminars

    Software
    Contact Us
    For Students
    Copyright (C) 2022
    The University of Texas Medical Branch
    Please Review Our
    Site Policies & Required Links
    Webmaster • Mark A. White