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

Finding Legacy Code SinCris. Some of the sites pointed to have closed down Legacy Code - Conclusions If it is well-liked and much-used, someone will maintain it. Command-line I/O is most easily maintained. If it has complicated I/O or a proprietary GUI, it will probably die. Good code can supplement published work. Code without manuals is almost valueless. Code with good commenting is valuable. Don’t re-invent the wheel. Build better ones. Page 46
Outline Complete rewrites When, why, and how? James W. Pflugrath 1 Rigaku/MSC, Inc., The Woodlands, Texas, USA • Previous software packages • Current software packages • When & Why Whenever you get a benefit and the money to do it Hardware requirements Software requirements • How Modern software engineering practices in scientific programming • Example • Future software packages • Bottom line Whenever you get a benefit Code maintenance Ego Previous software packages Previous software packages • FRODO, Alwyn Jones, 1970’s Evans & Sutherland PS300 version 1983 • MADNES, w/ A. Messerschmidt, , 1984 FORTRAN77, structured (no GOTOs) VAX/VMS, IRIX, Sun4, Linux, OSF1 Device-independent Enraf-Nonius FAST, ADSC multiwire, Xentronics EEC-workshops, 1980’s Vectorial description & algorithms, David Thomas Department of Energy, Beamline X8C, E. Westbrook early 1990s Current software packages • JWP moves to Molecular Structure Corporation, 1994 • d*TREK: device-independent independent diffraction image processing DOE subcontract, 1994, E. Westbrook Simple re-write or adaptation not possible • C++ Object-oriented programming language No standard template library • 1994 • Anytime! (2005) When & why? • Whenever a benefit or advantage arises from the re-write This is always the case, you would not make a worse piece of software would you? Page 47
Page 1 and 2: Commission on Crystallographic Comp
Page 3 and 4: CompComm Chairman’s Message This
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: Learning from the Past Learning fro
Page 49 and 50: Example: d*TREK • User interface
Page 51 and 52: One last thing … “Remember, sof
Page 53 and 54: Coordinate Systems: Real space Frac
Page 55 and 56: Coordinate Systems: Real space Othe
Page 57 and 58: Coordinate Systems: Operators Rotat
Page 59 and 60: Coordinate Systems Summary: In c
Page 61 and 62: Map probability phasing: Getting a
Page 63 and 64: Image enhancement using local featu
Page 65 and 66: Iterative model-building and refine
Page 71 and 72: 1 general introduction to suites Pr
Page 73 and 74: CCP4 runs on all commonly used plat
Page 75 and 76: Basic CCP4 directory hierarchy $CCP
Page 77 and 78: Pros & cons of scripting Pros • E
Page 79 and 80: Multi-step processes are toughwithG
Page 81 and 82: Even worse Even worse Even worse Co
Page 83 and 84: Page.5 © 2005 Bruker AXS BV. All R
Page 85 and 86: Page.13 © 2005 Bruker AXS BV. All
Page 95 and 96: Page.1 © 2005 Bruker AXS BV. All R
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Page.9 © 2005 Bruker AXS BV. All R
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Page.17 © 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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Page 167
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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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