Computational Crystallography Newsletter

Presenting information of general interest to the protein crystallography community.

Issues

Current issue

January 2016

Short Communications

  • Characterization of base pair geometry
  • Visual representations of internal coordinate restraints: Advantages and limitations

    Fitting tips #11 – Can a helical DNA basepair be Hoogsteen?

  • Previous Issues

    2015

    January 2015

    Articles

  • Improved Probabilistic Estimates of Biocrystal Solvent Content
  • Rapid evaluation of non-bonded overlaps in atomic models

    Short Communications

  • Plan a SAD experiment, scale SAD data, and analyze your anomalous signal
  • Validation of carbohydrate structures in CCP4 6.5
  • Disulfide bond restraints

    Fitting Tip #9: Avoiding excess cis peptides at low resolution or high B

    FAQ - Tips for coordinated metal refinement  

  • July 2015

    Articles

  • A context-sensitive guide to RNA & DNA base-pair & base-stack geometry

    Short Communications

  • New Phaser-MR search panel in Phenix
  • Quantum chemical techniques for minimising ligand geometries in the active site
  • 13 typical occupancy refinement scenarios and available options in phenix.refine

    Fitting tips #10 – How do your base pairs touch and twist?

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    2014

    January 2014

    Articles

  • FEL Detectors and ImageCIF
  • Quantum Mechanics-based Refinement in Phenix/DivCon

    Short Communications

  • Phenix tools for interpretation of BIOMT and MTRIX records of PDB files
  • Coping with BIG DATA image formats: integration of CBF, NeXus and HDF5

    Fitting tips #7 – Getting the Pucker Right in RNA Structures

  • July 2014

    Articles

  • Details of the Conformation-Dependent Library

    Short Communications

  • Connectivity analysis tools in CCTBX
  • phenix.fab_elbow_angle: Fragment Antigen-Binding elbow angle calculation tool

    Fitting tips #8 – Acetyl Groups are like Peptides: Planar and trans

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    2013

    January 2013

    Articles

  • cctbx tools for transparent parallel job execution in Python. I. Foundations
  • cctbx tools for transparent parallel job execution in Python. II. Convenience functions for the impatient.

    Short communications

  • Phenix / MolProbity Hydrogen Parameter Update
  • PSI SBKB Technology Portal: A Web Resource for Structural Biologists

    Fitting Tips #5: What's with water?

    FAQ - I'm seeing a lot of CIF files. Are they all restraints?

  • July 2013

    Articles

  • cctbx tools for transparent parallel job execution in Python. III. Remote access
  • phenix.ensemble_refinement: a test study of apo and holo BACE1

    Short Communications

  • CaBLAM: Identification and scoring of disguised secondary structure at low resolution
  • Structural Classification of Allergen IgE Epitopes by Hierarchical Clustering
  • New Tool: phenix.real_space_refine

    Fitting tips #6 - Potential misfitting by a switch of sidechain vs mainchain

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    2012

    January 2012

    Articles

  • CCTBX tools for derivative-free optimization
  • phenix.find_alt_orig_sym_mate
  • Using force field generated models in the refinement of crystallographic structures containing carbohydrates
  • Viewing diffraction images in CCTBX
  • On contribution of hydrogen atoms to X-ray scattering

    Fitting Tips #3: Importance of His flips

  • July 2012

    Articles

  • cctbx tools for transparent job execution on clusters
  • On the analysis of residual density distributions on an absolute scale

    Short communications

  • DETAC: tools to detect alternative conformations by unrestrained refinement
  • ERRASER, a powerful new system for correcting RNA models

    Fitting Tips #4: Rotamer correction with backrubs

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    2011

    January 2011

    Articles

  • Fuzzy space group symbols: H3 and H32
  • Visualizing the raw diffraction pattern with LABELIT
  • Electron density illustrations
  • Maximum likelihood refinement for twinned structures
  • TLS for dummies

    Short communications

  • Multi-criterion kinemage graphics in PHENIX
  • phenix.ensembler: a tool for multiple superposition
  • phenix.mr_rosetta: a new tool for difficult molecular replacement problems

    Fitting Tips #1: Not 3 parallel COs in β

  • July 2011

    Articles

  • Improved target weight optimization in phenix.refine
  • Mite-y lysozyme crystal and structure

    Short communications

  • A lightweight, versatile framework for visualizing reciprocal-space data
  • An extremely fast spotfinder for real-time beamline applications
  • Hints for running phenix.mr_rosetta

    Fitting Tips #2: Hi-res geometry outliers

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    2010

    July 2010

    Articles

  • cctbx PDB handling tools
  • Secondary structure restraints in phenix.refine
  • cctbx Spotfinder: a faster software pipeline for crystal positioning
  • On atomic displacement parameters (ADP) and their parameterization in PHENIX

    Short communications

  • Non-periodic torsion angle targets in PHENIX
  • Model building updates & new features
  • Author Resources

    Word template

    Contact the editor: Nigel W. Moriarty