Computational Crystallography Newsletter

Presenting information of general interest to the protein crystallography community.

Current Issue

January 2021


  • HKLviewer, a new 3D reflection data viewer for CCTBX
  • Running CCTBX and PyMOL in the same Jupyter Notebook

    Short Communications

  • PDB50: Celebrating 50 Years of the Protein Data Bank in 2021
  • Lessons from using the Cambridge Structure Database: II – Element specification X/Z
  • The Importance of Being Positive: Charged ligands that bind nucleic acids

    Fitting tips #20 – In-plane or out-of-plane H atom placement on the edges of aromatic rings

  • Popular articles

  • 13 typical occupancy refinement scenarios and available options in phenix.refine — Afonine, P.V. (2015). Comput. Crystallogr. Newsl. 5, 37-46.
  • FAQ - I'm seeing a lot of CIF files. Are they all restraints? — Gildea, R.J., Moriarty, N.W. & Adams P.D. (2013). Comput. Crystallogr. Newsl. 4, 6-8.
  • Visual representations of internal coordinate restraints: Advantages and limitations — Afonine, P.V. & Moriarty, N.W. (2016). Comput. Crystallogr. Newsl. 7, 10-14.
  • Editor's note about "Human Readable PDB Codes" — Moriarty, N.W. (2015). Comput. Crystallogr. Newsl. 6, 26.


    Expert Advice FAQ


    January 2020


  • Ensemble refinement produces consistent R-free values but smaller ensemble sizes than previously reported
  • dtmin - a Domain Tunable Python Minimizer

    Short Communications

  • phenix.homology: finding high-resolution matches for low-resolution models at a chain level
  • Lessons from using the Cambridge Structure Database: I – Bond number specification

    Fitting tips #19 – Remember to use the information from NCS copies

    FAQ - Can I control the automatic linking?

  • July 2020

    Not produced.



    January 2019

    Short Communications

  • MARCO: The Machine Recognition of Crystallization Outcomes
  • Building a model the way you do: Map-to-model version 2

    Fitting tips #17 – Asn and Gln are remarkably different

    FAQ - Are the defaults the best for refinements?

  • July 2019


  • Processing serial crystallographic data from XFELs or synchrotrons using the cctbx.xfel GUI

    Short Communications

  • Automatic β-peptide linking in Phenix
  • phenix.hbond: a new tool for annotation hydrogen bonds
  • Bytes and Bobs : Accelerating python code with Numba

    Fitting tips #18 – A subversive kind of misfit “water”

    FAQ - Can I submit my X-ray model to the Protein Data Bank in PDB format?



    January 2018


  • Cβ deviations and other aspects in Amber versus CDL refinements
  • A few benchmark tests of various compilers on Linux and Windows

    Short Communications

  • Tools for model-building with cryo-EM maps
  • Gemmi – a new MX library
  • Overfitting to Ramachandran and geometry criteria in the cryoEM Model Challenge

    Fitting tips #15 – New help to make your 2.5–4Å cryoEM structure even better

    FAQ - What happens when the Phenix GUI prompts me to send an error report?

  • July 2018


  • Using the New Program Template

    Short Communications

  • CaBLAM: A C-Alpha Based Low-resolution Annotation Method for secondary structure and validation
  • Tools for interpreting cryo-EM maps using models from the PDB

    Fitting tips #16 – Vicinal disulfides: Have you seen one of these strange gems?

    FAQ - How do I model a partially broken disulphide?



    January 2017


  • Deploying cctbx.xfel in Cloud Computing and High Performance Computing Environments

    Short Communications

  • multi_core_run(), yet another simple tool for embarrassingly parallel jobs
  • Phenix tool to compute a difference map for cryo-EM

    Fitting tips #13 – O-pairs: The love-hate relationship of carboxyl oxygens

  • July 2017

    Short Communications

  • phenix.mtriage: a tool for analysis and validation of cryo-EM 3D reconstructions
  • More TLS validation with phenix.tls_analysis

    Fitting tips #14 – How Ser & Thr behave oddly on helices

    FAQ - What is in the MTZ output by phenix.refine?



    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?

    FAQ - Why can't I see the link I want in my model?

  • July 2016


  • Working with EIGER data
  • Processing XFEL data with cctbx.xfel and DIALS

    Short Communications

  • Using Molecular Dynamics Simulations to Enrich the Water Structure in Biomolecular Crystals

    Fitting tips #12 – Twist Tells: better β strands at >3.5Å in x-ray or cryoEM

    FAQ - Why is the documentation on the website different from what I’m seeing in my installation?



    January 2015


  • 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 tips #9 – Avoiding excess cis peptides at low resolution or high B

    FAQ - Tips for coordinated metal refinement

  • July 2015


  • 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?



    January 2014


  • 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


  • 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



    January 2013


  • 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


  • 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

    FAQ - After I refine my model, why isn't atom X bound to atom Y when I look at it in a molecular viewer?



    January 2012


  • CCTBX tools for derivative-free optimization

    Short Communications

  • 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

    FAQ - What Molprobity score is acceptable?

  • July 2012


  • 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

    FAQ - How can I use semi-emperical quantum chemical methods to optimise the geometry of my ligand?



    January 2011


  • 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

    FAQ - There are two methods to add links between atoms in PHENIX. Which one should I use?

  • July 2011


  • 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

    FAQ - How do I make composite omit maps in PHENIX?

    July 2010


  • 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

    Expert Advice Geometry

    FAQ - How

  • Author Resources

    Word template Author Index

    Contact the editor: Nigel W. Moriarty