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$Rietveld Refinement from Powder Diffraction Data - Max Planck ...$

Refinement II - Modern Developments 168 Dale E. Tronrud CCP14 workshop Notes: On Minimization Targets and Algorithms 171 Dale E. Tronrud Computational aspects of the Rietveld Method 176 Juan Rodríguez-Carvajal Statistical Treatment of Uncertainties 183 Dale E. Tronrud Programming pdCIF and Rietveld 187 Brian H. Toby Structure Comparison, Analysis and Validation 194 Ton Spek Testing software 202 Harry Powell The future of direct methods 206 George M. Sheldrick CrysFML: A crystallographic library in modern Fortran 271 Juan Rodríguez-Carvajal Connecting to hardware 280 Rob Hooft Tcl/Tk demo 286 Brian Toby CCTBX Unit Cell Refinement Tutorial 292 Ralf W. Grosse-Kunstleve CCTBX Direct Methods Tutorial 303 Ralf W. Grosse-Kunstleve CCTBX Central Types 317 Ralf W. Grosse-Kunstleve Tutorial on scoring methods for evaluation of electron density maps 318 Tom Terwilliger Siena 2005 IUCr Computing School Tutorials : Calls for contributions to Newsletter No. 7 323 Using the Clipper libraries 210 Kevin Cowtan Exercises in map manipulation 220 Kevin Cowtan Reciprocal Space Tutorial (RST) 224 George M. Sheldrick Fortran 77 solution to GMS RST 229 George M. Sheldrick C++ solution to GMS RST 232 Tim Gruene C++ solution to GMS RST 239 Michel Fodje Fortran 95 solution to GMS RST 247 Juan Rodríguez-Carvajal Java solution to GMS RST 252 Bradley Smith Fortran solution to GMS RST 258 Stephan Ruehl Initial Python solution to GMS RST 269 Ralf W. Grosse-Kunstleve Slightly Enhanced Python solution to GMS RST 270 Ralf W. Grosse-Kunstleve Page 2
CompComm Chairman’s Message This newsletter makes the presentations available to a wider audience of the lectures given at the IUCr Crystallographic Computing School 2005 in Siena, prior to the Florence 2005 IUCr congress. This breaks with a tradition of the past where, based on the material presented, a very expensive book was produced with rather limited distribution. We hope that the current approach that we have choosen for the distribution of the lecture material fits more in our 'Google-age', where a lot of information is now looked for on the WEB. One of the implicit themes during this meeting was the software language to be used for future software development. Traditionally, Fortran in its various incarnations was the default language. A large number of programs that are in use today are written in that language (e.g. the SHELX suite). Fortran could still be the language of choice today for scientific computing in view of its simplicity and efficiency. However, computing science has now moved to C-type and scripting languages, of which C++ and Python are currently the most popular respectively. A large number of libraries for graphical user interfaces are currently available for those languages. C++ will be the de-facto language of the future, notwithstanding its sharp learning curve. Interestingly, George Sheldrick (one of the lecturers and a longstanding Fortran addict like me) has now taught himself C++ as an outcome of this very successfull school. I would like to thank the speakers again for all the work they did to prepare their presentations, the sponsors for their financial support, my co-organisers, the University of Siena for making available an excellent meeting site and Prof. Marcello Mellini for making it all work locally. Ton Spek, Chairman of the IUCR computing school and IUCr Computing Commission, (a.l.spek@chem.uu.nl ) Newsletter No. 6 This newsletter collates the notes from the Siena 2005 IUCr Crystallographic Computing School. The individual files are located on the school webpage at: http://www.iucr.org/iucr-top/comm/ccom/siena2005/notes.html The next edition of the newsletter is expected to get back to the usual format with an intended theme involving “Minimisation” algorithms for indexing, structure solution and refinement. It should hopefully appear around April 2006. Lachlan Cranswick, (lachlan.cranswick@nrc.gc.ca) Page 3
Page 1: Commission on Crystallographic Comp
Page 5 and 6: Participants of the IUCr Computing
Page 7 and 8: Direct Methods Meetings • Many pa
Page 9 and 10: Problem from Symbolic Addition Meth
Page 11 and 12: Thanks to our Sponsors ! • Bruker
Page 13 and 14: Porting Existing Software Used to b
Page 15 and 16: Command-line interfaces - old-fashi
Page 17 and 18: Don’t re-invent the wheel unneces
Page 19 and 20: Evolution of programming languages
Page 21 and 22: Automatic memory management • Con
Page 23 and 24: Louis Farrugia - IUCr Computing Sch
Page 31 and 32: Vector operations • Computer Scie
Page 33 and 34: 6. Finding solutions to singulariti
Page 35 and 36: Obsolete Legacy Code Re-inventing t
Page 37 and 38: Uses of Legacy Code - Design Wider
Page 39 and 40: Uses of Legacy Code Data Representa
Page 41 and 42: Uses of Legacy Code - Design Singul
Page 43 and 44: Matrix of Constraint ‘Riding’ a
Page 45 and 46: Learning from the Past Learning fro
Page 47 and 48: Outline Complete rewrites When, why
Page 49 and 50: Example: d*TREK • User interface
Page 51 and 52: One last thing … “Remember, sof
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Coordinate Systems: Real space Frac
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Coordinate Systems: Real space Othe
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Coordinate Systems: Operators Rotat
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Coordinate Systems Summary: In c
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Map probability phasing: Getting a
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Image enhancement using local featu
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Iterative model-building and refine
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Louis Farrugia - IUCr Computing Sch
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Louis Farrugia - IUCr Computing Sch
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1 general introduction to suites Pr
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CCP4 runs on all commonly used plat
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Basic CCP4 directory hierarchy $CCP
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Pros & cons of scripting Pros • E
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Multi-step processes are toughwithG
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Even worse Even worse Even worse Co
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Page.5 © 2005 Bruker AXS BV. All R
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Page.13 © 2005 Bruker AXS BV. All
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Stanton, et al. (1992) J. Appl. Cry
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Refine (crystal mosaicity) Refine (
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Integrate - Profile fitting Integra
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Goals of the Talk Atomic pair distr
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MI(T) transition is polaronic local
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History Disordered Carbon Warren, B
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Applications are networks of compon
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Useful book http://nirt.pa.msu.edu/
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Proteins and powders Proteins and p
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Comparing paracetamol trihydrate st
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Complex anisotropic sample line-sha
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Input Files Input files are: 1. A p
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DEFINE SOLVENT ACCESSIBLE VOID DEFI
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Ideas behind the Algorithm Possible
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Simple algorithms for macromolecula
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Density modification The heavy atom
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Automation of structure determinati
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Evaluating electron density maps Me
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Chain extension by placement of tri
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Automation of structure determinati
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Crystallographic symmetry: Space gr
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Crystallographic symmetry: Maps Map
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Crystallographic symmetry: hkl Reci
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Profile refinement Least-squares an
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What’s gone wrong? • We’ve pe
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Part III What if there’s an impur
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20% Y 2 O 3 : robust refinement 100
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with thanks … M Brunelli, A N Fit
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Understanding Likelihood Example:
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Understanding Likelihood Understand
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Likelihood and Crystallography But
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A more complicated example of the s
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Refinement and Rebuilding On Minimi
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Difficulties in Maximum Likelihood
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Who’s Got What? Full matrix refi
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I y I ( T T ) b ci h i h i {h}
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Needs for precise refinements and m
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Skeleton of the Rietveld algorithm
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Introduction Statistical Treatment
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Maximum Likelihood Finding the mos
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Talk Outline Programming pdCIF and
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CIF Dictionaries CIF definitions ar
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GSAS2CIF: Solutions • Divide Acta
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Specify plot contents Page 193
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Intra-Molecular (Continued) • Det
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“Orthorhombic” Polymorph Tetrag
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Validation with PLATON - Details: w
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Consult the CSD • It is a good id
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You may want an identical result if
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Profiling: use an external program
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The Multan Era (1969-1986) The prog
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Disulfide bond resolution When the
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Clipper libraries Clipper libraries
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Clipper Libraries: In detail Crysta
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Clipper libraries Data objects: Re
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Clipper libraries Data objects: I
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Clipper libraries Expanding data to
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Map manipulation Skeletonisation:
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Map manipulation Skeletonisation: M
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The hidden trap If the floating poi
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Equivalents in P4 1 2 1 2 For P4 1
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D:\tmp\gs_tutorial_code\gsm_data_an
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D:\tmp\gs_tutorial_code\gsm_data_an
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D:\tmp\gs_tutorial_code\tim_gruene_
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D:\tmp\gs_tutorial_code\michel_fodj
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D:\tmp\gs_tutorial_code\juan_rc_f95
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package reflectionSort; import java
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private void setIfStandardHkl(Mille
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D:\tmp\gs_tutorial_code\stephan_rue
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D:\tmp\gs_tutorial_code\ralf_gk_pyt
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CrysFML: A crystallographic library
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Scope of CrysFML We have developed
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Example of BasIreps output: *.bsr +
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Output of the small program: Get_SP
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Installing and compiling CrysFML us
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Socket programming To complete this
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} char protocol[2]; char s_status[6
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mess = recvfixed(s, length) except
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looping foreach var {1 2 3 a b c} {
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• Nothing happens! Demo 4 - New c
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Unix/OS X proc forknewterm {title c
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Here two steps are combined into on
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we don't have to invent names for t
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Computation of the least-squares re
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class refinery: def __init__(self):
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Exercise (not very hard) Read the 2
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direct_methods_light.py Overview Th
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If the miller_array is an intensity
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print "number of large_e_values:",
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technical detail. A subsequent step
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xray_structure = acta_c.cif_as_xray
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correlation = flex.linear_correlati
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At this stage the peak_model object
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Central cctbx types unit_cell compo
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Running AutoSol in PHENIX to phase
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Now reconsider what we are doing...
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Call for Contributions to the Next
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