Crystallography

TUTORIALS

ROCA-CSIC: Excelent introductory course to crystallography.

University of Cambridge: Protein Crystallography Course.

B. RUPP: CRYSTALLOGRAPHY 101.

K. Cowtan: Teaching materials.

Scottlab: Teaching materials+software installation

• Homebrew: Package manager for macOS or Linux

DATA ADQUISITION, REDUCTION AND SCALE

Mosflm: Manual and program for different OS.

XDS: X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method.

• XDSwiki
• XDSAPP: A graphical user interface for data processing using XDS

HKL2000: Denzo, XDisplayF and Scalepack.

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AnisoScale: Diffraction Anisotropy Server for the detection and treatment of data anisotropy.

Twinning: Twin detection from collected intensities

PHASE CALCULATION AND REFINEMENT

CCP4: Programs suite for handling x-ray diffraction data. Scaling (Scala), MR (Molrep, Amore, Phaser) and refinement (Refmac), and many other utilities.

• CCP4wiki
• TLS Motion Determination: Translation/Libration/Screw vibrational motion.

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.

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Matthews coefficient: Server that calculates normalized probabilities for the Vm (Matthews coefficient) and solvent content (Vs).

PARVATI: Protein Anisotropic Refinement Validation and Analysis Tool.

ChEBI: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

JLigand: Make your own ligand.

• Tutorial

CheckMyBlob: Identify & Validate your ligands.

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

CIF editor (PDBj): Edit mmCIF and validate the data entered.

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PDB_REDO: Is a tool for macromolecular X-ray crystallographers who wish to optimize the refinement of their structure.

GRAPHICS

Coot: Macromolecular model building, model completion and validation. (CCP4wiki-COOT: Instalation, scripts, etc.)

• RCrane: Allows for semi-automated building of RNA structure within Coot.

PyMOL: Is a molecular visualization system. (Pymol-wiki)

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.

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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. .

LigPlot: Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file. (LigPlot+: NEW multiple ligand-protein interaction diagrams for drug discovery.)

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.

Multiple structure superposition

3D-SS: 3-Dimensional structural superposition

MATRAS: Protein 3D Structure Comparison

SuperPose: Protein superposition server

MultiProt: It finds the common geometrical cores between the input molecules.

PDBeFold: Structure Similarity

VALIDATION

wwPDB servers: Stand-alone wwPDB validation servers.

• Notes: Explanation on how to interpret the validation report.

• PDB-extracts: Files preparation for PDB deposition including conversion to mmCIF format.

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.

JCSG Structure Validation Central: This server performs quality checks using Procheck,SFCheck, etc.

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DSSP: Secondary structure assignment.

Stride: Server that offers an interactive interface to the secondary structure assignment.

• DSSP/HSSP: The CMBI DSSP/HSSP server.
• 2Struc: Server to determined SS using different methods.

DSSR: A program for Defining the Secondary Structures of RNA from three-dimensional coordinates.

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CheckMyMetal (CMM): Metal Binding Site Validation Server.

INTER & INTRAMOLECULAR CONTACTS, ETC.

PSAP: A web based suite for protein structure analysis.

VADAR: Single (or Multiple) Model Protein Structure 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.

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