ROCA-CSIC: Excelent introductory course to crystallography.
University of Cambridge: Protein Crystallography Course.
B. RUPP: CRYSTALLOGRAPHY 101.
K. Cowtan: Teaching materials.
Mosflm: Manual and program for different OS.
XDS: X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method.
HKL2000: Denzo, XDisplayF and Scalepack.
AnisoScale: Diffraction Anisotropy Server for the detection and treatment of data anisotropy.
Twinning: Twin detection from collected intensities
CCP4: Programs suite for handling x-ray diffraction data. Scaling (Scala), MR (Molrep, Amore, Phaser) and refinement (Refmac), and many other utilities.
Phenix: Programs suite base on Python for Integrated Xtallography.
SHELX: Is a set of programs for the determination crystal structures by single crystal X-ray/neutron diffraction.
ARP-WARP: Automatic protein model tracing and building. It is integrated within CCP4 and Phenix.
OLDERADO: The reports include identification of the most representative NMR model and clusters within the ensemble.
Auto-Rickshaw: Automated crystal structure determination platform.
Anomalous Scattering Coefficients: Forms interface to plot theoretical values of f' and f".
MR-MEX: Molecular Replacement by Replica-EXchange Monte Carlo simulation.
Matthews coefficient: Server that calculates normalized probabilities for the Vm (Matthews coefficient) and solvent content (Vs).
PARVATI: Protein Anisotropic Refinement Validation and Analysis Tool.
HICUP: Data base of ligands, prostetic groups, cofactors, etc. Provides parameters and coordinates files for many refinement programs.
JLigand: Make your own ligand.
Grade: Grade Server generates geometrical restraints for novel small molecules.
PRODRG: Description of a small molecule. It'll generate a variety of topologies and energy-minimized coordinates in a variety of formats.
MolInspiration: Cheminformatics on the Web
PDB_REDO: Is a tool for macromolecular X-ray crystallographers who wish to optimize the refinement of their structure.
Deep View: Swiss-PdbViewer: is an visualization application allowing to analyze several proteins at the same time.
MolScript: For displaying molecular 3D structures in both schematic and detailed representations.
Chimera: is a visualization program that allows the visualization and analysis of molecular structures and related data i.e. density maps, assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
PDBsum: It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of the interactions between them. .
TopDraw: Is a sketchpad for drawing topology cartoons of proteins
Pro-Origami: Is a system for automatically generating protein structure cartoons.
3D Protein Structure & Kinemage Home Page: Is a scientific illustration presented as an interactive computer display with several development very useful tools for crystallography.
3D-SS: 3-Dimensional structural superposition
MATRAS: Protein 3D Structure Comparison
MultiProt: It finds the common geometrical cores between the input molecules.
PDBeFold: Structure Similarity
wwPDB servers: Stand-alone wwPDB validation servers.
QC: The QC server reports the stereochemical quality of the model using AutoDepInputTool, MolProbity, and Phenix.
MolProbity: All-atom contact, conformation, and geometry analysis.
WHAT IF: Molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
STAN: The STructure ANalysis server.
PDB_REDO: This server is a tool for macromolecular X-ray crystallographers to optimize the refinement of their structure.
DSSP: Secondary structure assignment.
Stride: Server that offers an interactive interface to the secondary structure assignment.
DSSR: A program for Defining the Secondary Structures of RNA from three-dimensional coordinates.
CheckMyMetal (CMM): Metal Binding Site Validation Server.
CryCo: CRYstal COntact Analysis.
PISA: Tool for the exploration of macromolecular interfaces.
PIC: The Protein Interactions Calculator evaluate disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, etc. within a protein or between proteins in a complex.
WAP: Water Analysis Package.