January 2019

Full issue

• 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

Full issue

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

• 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

Full issue

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

• 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

Full issue

• Using the New Program Template

• 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

Full issue

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

• 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

Full issue

• 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

Full issue

• 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

Full issue

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

• 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

Full issue

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

• 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

Full issue

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

• 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

Full issue

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

• 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

Full issue

• Details of the Conformation-Dependent Library

• 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

Full issue

• 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.

• 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

Full issue

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

• 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

Full issue

• 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

• FAQ - What Molprobity score is acceptable?

July 2012

Full issue

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

• 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

Full issue

• 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

• 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

Full issue

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

• 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?