Computational Crystallography Newsletter
The newsletters describe topics of general interest to the protein crystallography community.
Current Issue: January 2022
- Extreme backbone outlier patterns when AlphaFold gives up
- Difference Density Tracer: A Tool for Rapid Visualization of Difference Densities in Proteins to identify Dynamics
- 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.
- HKLviewer, a new 3D reflection data viewer for CCTBX
- Running CCTBX and PyMOL in the same Jupyter Notebook
- 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
- The effect of adding a single peptide bond class
- The top2018 pre-filtered dataset of high-quality protein residues
- Updates from the Worldwide PDB: Celebrating PDB50 and PDBx/mmCIF news
- Lessons from using the Cambridge Structure Database: III – Outlier Rejection
- Ensemble refinement produces consistent R-free values but smaller ensemble sizes than previously reported
- dtmin - a Domain Tunable Python Minimizer
- 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
- MARCO: The Machine Recognition of Crystallization Outcomes
- Building a model the way you do: Map-to-model version 2
- Automatic β-peptide linking in Phenix
- phenix.hbond: a new tool for annotation hydrogen bonds
- Bytes and Bobs : Accelerating python code with Numba
- 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
- 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
- multi_core_run(), yet another simple tool for embarrassingly parallel jobs
- Phenix tool to compute a difference map for cryo-EM
- Characterization of base pair geometry
- Visual representations of internal coordinate restraints: Advantages and limitations
- 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
- 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
- Phenix tools for interpretation of BIOMT and MTRIX records of PDB files
- Coping with BIG DATA image formats: integration of CBF, NeXus and HDF5
- Connectivity analysis tools in CCTBX
- phenix.fab_elbow_angle: Fragment Antigen-Binding elbow angle calculation tool
- 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
- 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
- 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
- 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
- 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
- A lightweight, versatile framework for visualizing reciprocal-space data
- An extremely fast spotfinder for real-time beamline applications
- Hints for running phenix.mr_rosetta
- 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
- Fitting tips #21 – What are chiral outliers and what can I do about them?
- Fitting tips #20 – In-plane or out-of-plane H atom placement on the edges of aromatic rings
- Fitting tips #19 – Remember to use the information from NCS copies
- Fitting tips #18 – A subversive kind of misfit “water”
- Fitting tips #17 – Asn and Gln are remarkably different
- Fitting tips #16 – Vicinal disulfides: Have you seen one of these strange gems?
- Fitting tips #15 – New help to make your 2.5–4Å cryoEM structure even better
- Fitting tips #14 – How Ser & Thr behave oddly on helices
- Fitting tips #13 – O-pairs: The love-hate relationship of carboxyl oxygens
- Fitting tips #12 – Twist Tells: better β strands at >3.5Å in x-ray or cryoEM
- Fitting tips #11 – Can a helical DNA basepair be Hoogsteen?
- Fitting tips #10 – How do your base pairs touch and twist?
- Fitting tips #9 – Avoiding excess cis peptides at low resolution or high B
- Fitting tips #8 – Acetyl Groups are like Peptides: Planar and trans
- Fitting tips #7 – Getting the Pucker Right in RNA Structures
- Fitting tips #6 – Potential misfitting by a switch of sidechain vs mainchain
- Fitting tips #5 – What's with water?
- Fitting tips #4 – Rotamer correction with backrubs
- Fitting tips #3 – Importance of His flips
- Fitting tips #2 – Hi-res geometry outliers
- Fitting tips #1 – Not 3 parallel COs in β
- Geometry restraint ESD
FAQ - Can I control the automatic linking?
FAQ - Are the defaults the best for refinements?
FAQ - Can I submit my X-ray model to the Protein Data Bank in PDB format?
FAQ - What happens when the Phenix GUI prompts me to send an error report?
FAQ - How do I model a partially broken disulphide?
FAQ - What is in the MTZ output by phenix.refine?
FAQ - Why can't I see the link I want in my model?
FAQ - Why is the documentation on the website different from what I’m seeing in my installation?
FAQ - Tips for coordinated metal refinement
FAQ - I'm seeing a lot of CIF files. Are they all restraints?
FAQ - After I refine my model, why isn't atom X bound to atom Y when I look at it in a molecular viewer?
FAQ - What Molprobity score is acceptable?
FAQ - How can I use semi-emperical quantum chemical methods to optimise the geometry of my ligand?
FAQ - There are two methods to add links between atoms in PHENIX. Which one should I use?
FAQ - How do I make composite omit maps in PHENIX?
FAQ - How do I create restraints for my ligand in PHENIX?