not retired: hall symbols + cif or how syd influenced my life without me noticing it. ralf w....
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Not retired: Hall symbols + CIFor
How Syd influenced my life without me noticing it.
Ralf W. Grosse-Kunstleve
Computational Crystallography InitiativeLawrence Berkeley National Laboratory
White-Hall Retirement Symposium, July 16/17, 2007
My connections to Syd
• PhD project: Zeolite structure determination from powder data using extracted intensities– focus– sginfo: Hall symbols
• Contributions to Xplor/CNS– Joined Axel Brunger’s group encouraged by Syd (ECM
1995)– Single-crystal protein crystallography– About 80% of all PDB entries refined with Xplor/CNS– CNS PDB deposition via mmCIF files
• Phenix project– Automation of protein structure determination– Fresh start after losing a legal battle– The P in Phenix is for Python: recommended by Syd
Concise space group symbols
• Symbols for crystallographic space groups• Designed to overcome limitations of the familiar Hermann-
Mauguin symbols (e.g. P 21 21 21)
• H-M symbols are defined in International Tables for Crystallography– Created by a generation of scientist that didn’t have computers
• Define the space group type uniquely
• But not the exact setting: inadequate for automatic processing• Attempts to add a rule set to H-M symbols leads to
complicated algorithms (never standardized)• H-M symbols cover only a very limited subset of settings that
appear, e.g. in the generation of group-subgroup relations
Hall (1981) symbols
• Symbols for crystallographic space groups• Designed to overcome limitations of the familiar Hermann-
Mauguin symbols (e.g. P 21 21 21)
• H-M symbols are defined in International Tables for Crystallography– Created by a generation of scientist that didn’t have computers
• Define the space group type uniquely
• But not the exact setting: inadequate for automatic processing• Attempts to add a rule set to H-M symbols leads to
complicated algorithms (never standardized)• H-M symbols cover only a very limited subset of settings that
appear, e.g. in the generation of group-subgroup relations
Hall symbols
• Designed for automatic processing– No ambiguities
• Via attached transformation symbols, any setting of any crystallographic space group can be represented (Int. Tab. Vol. B, 2001)
• Applications– Determination of space group type– Automatic determination of allowed origin shifts– Automatic group-subgroup processing– Automatic derivation of twin laws– Primitive setting of centered space groups
• Reduces memory requirements
Translation table Hall Hermann-Mauguin/* 081 */ " P -4", /* P -4 *//* 082 */ " I -4", /* I -4 *//* 083 */ "-P 4", /* P 4/m *//* 084 */ "-P 4c", /* P 42/m *//* 085 */ "-P 4a", /* P 4/n :2 *//* 086 */ "-P 4bc", /* P 42/n :2 *//* 087 */ "-I 4", /* I 4/m *//* 088 */ "-I 4ad", /* I 41/a :2 *//* 089 */ " P 4 2", /* P 4 2 2 *//* 090 */ " P 4ab 2ab", /* P 4 21 2 *//* 091 */ " P 4w 2c", /* P 41 2 2 */
STAR + CIF
• Situation before CIF– Vast, diverse variety of data formats– Need to reformat data all the time is a real impediment to scientific
progress– What does “gof” mean?– What does it mean exactly?
• STAR: Self-defining Text Archival and Retrieval format• Hall, S. R., "The STAR File: A New Format for Electronic Data Transfer and
Archiving," J. Chem. Inf. Comput. Sci. 31, 326-333 (1991).
– Defines format– Framework for defining semantics
• CIF (1991)– Based on STAR, defines semantics– Similar in concept to XML schema, but a decade ahead– CIF is de-facto standard in small molecule crystallography– Macromoleclar community has more difficulties with the
semantics part of CIF
Python
• Situation: forced end of CNS development– Legal reasons
• Axel Brunger wanted Paul Adams and me to continue methods development in a different way
• We started exploring the world around us– We wanted a scripting language like CNS with
additional compiled components
• IUCr meeting Glasgow 1999– Watching solar eclipse with Syd– BTW: use Python
The PHENIX project
Funding: NIH Program Project (NIGMS, PSI), Director - Paul Adams
A collaboration between several groups
CCI APPS
SOLVE / RESOLVE
PHASER
TEXTAL
MolProbity / REDUCE
Computational Crystallography Initiative (LBNL)-Paul Adams, Ralf Grosse-Kunstleve, Pavel Afonine-Nigel Moriarty, Nicholas Sauter, Peter Zwart
Los Alamos National Lab (LANL)-Tom Terwilliger, Li-Wei Hung
Cambridge University -Randy Read, Airlie McCoy
Texas A&M University -Tom Ioerger, Jim Sacchettini, Erik McKee
Duke University - Jane Richardson, David Richardson, Ian Davis
Spectrum of phenix components
• Automated analysis of data quality: phenix.xtriage
• Rapid substructure determination: phenix.hyss
• Phasing: Maximum likelihood – SOLVE, PHASER for SAD
• Density modification: Statistical density modification (RESOLVE)
• Automated model building:– Pattern matching methods (RESOLVE or TEXTAL)
• Structure refinement: phenix.refine (likelihood, annealing, TLS)
• Advanced automation: AutoSol – hkl to map
• Ligand building and fitting: eLBOW, AutoLigand
• Validation and Hydrogens: MolProbity + Reduce
phenix.refine
- Group ADP refinement
- Rigid body refinement
- Restrained refinement (xyz, iso/aniso ADP)
- Automatic water picking
- Bond density
- Unrestrained refinement
- FFT or direct summation
- Hydrogens
- Automatic NCS restraints
- Simulated Annealing
- Occupancies (individual, group)
- TLS refinement
- Twinned data
- X-ray, Neutron, joint X-ray + Neutron refinement
Refinement flowchart
Input data and model processing
Refinement strategy selection
Bulk-solvent, Anisotropic scaling, Twinning parameters refinement
Ordered solvent (add / remove)
Target weights calculation
Coordinate refinement(rigid body, individual)
(minimization or Simulated Annealing)
ADP refinement(TLS, group, individual iso / aniso)
Occupancy refinement (individual, group)
Output: Refined model, various maps, structure factors, complete statistics
PDB model,Any data format (CNS, Shelx, MTZ, …)
Files for COOT, O, PyMol
Repeated several times
Summary
• Hall symbols open the door to automatic processing of crystallographic symmetry
• STAR + CIF enable automation of data flow between researchers and archives
• Our experience with Python suggests: it is a good idea to listen to Syd!
• Syd’s wisdom!… Gnu Xtal System, available as an open source project, … but with the expectation that Sourceforge may be its twilight resting place, afore it's entombed by the sands of time, right alongside The King of Kings.
Acknowledgments
• Syd– for shining the light in the right direction– for showing me Perth
• Phenix developers– P.D. Adams– P. Afonine– T.R. Ioerger– A.J. McCoy– E.W. McKee– N.W. Moriarty– R.J. Read– N.K. Sauter– J.N. Smith– L.C. Storoni– T.C. Terwilliger– P.H. Zwart
• Funding: – LBNL (DE-AC03-76SF00098)
– NIH/NIGMS (1P01GM063210)
– PHENIX Industrial Consortium