Building a teaching course around crystallographic freeware

1
Building a teaching course around
crystallographic freeware

• Lachlan M. D. Cranswick - CCP14 Project, UK and
• Geochemistry - Lamont-Doherty Earth Observatory
  of
• Columbia University, Palisades, New York, USA.
• E-mail lachlan_at_ldeo.columbia.edu
• WWW http//www.ldeo.columbia.edu/lachlan/
• WWW http//www.ccp14.ac.uk/

2
Main aim of this talk

• Emphasize that there is a range of high quality
  freely available software packages that can be
  useful for simple to advanced crystallographic
  teaching of single crystal and powder diffraction
• Encourage teachers of crystallography to consider
  continually checking for new software tools that
  can help teach not only scientific skills, but
  career employable scientific skills.
• Suggest that crystallographic teaching courses
  should also be training students on a diverse
  range of crystallographic software and
  encouraging versatility in the attitudes of
  students to continually search and use new tools
  and techniques as a continuing process of self
  education.

3
Notes Free Zone - they are on the
webhttp//www.ccp14.ac.uk/poster-talks/aca2001/
4
Why bother considering a variety of modern
software? (1 of 4)

• One consideration for modern crystallographic
  teaching is to minimize the risk of producing
  Crystallographic Cannon Fodder and maximize (i)
  employability of graduates and (ii) intellectual
  opportunities for obtaining an exciting
  scientific career.

5
Why bother considering a variety of modern
software? (2 of 4)

• Path of Most Resistance?
• Using a variety of state-of-the-art tools can
  improve students versatility by demonstrating
  different pathways to tackle crystallographic
  problems.
• When to use a subtle crystallographic nutcracker
• When to unlock the sledgehammer cabinet
• When to declare that Defcon 1 has been activated!

6
Why bother using and teaching a variety of
modern software? (3 of 4)Crystallographic
Weaponry 101

• Provide both
• i) a rigorous grounding in the theory and
• ii) the want in students to find and use the best
  software tools for the job
• Provide for chemists and scientists who use
  crystallography as a tool within a larger project
  and context.

7
Why bother using freely available software? (4
of 4)
Crystallographic Weaponry 102

• Much freely available software is state of the
  art in both algorithms and usability - (GUIs)
• Lessons can concentrate on the crystallography
  (rather than learning text editors)
• Can be installed on as many computers as you want
  - where-ever you like
• Students can take programs home and use on their
  personal computers (negate software piracy
  problems)
• Students can use the software as an initial
  research tool kit

8
Agenda for Some Examples

• Automatic structure solution and refinement
  Platon / System S
• Spacegroups and Symmetry using Gretep
• Scattering scatfac, dispano, poudrix,
  powder cell
• Peak profiles and peak profiling using XFIT
• Powder Indexing using Crysfire and Chekcell/
• Systematic absences in PXRD using Chekcell
• Complete single crystal analysis methods via
  WinGX
• Guided crystal structure refinement using
  Crystals
• Structure validation using Platon

9
Hopefully Platon / System S demonstration
worked!(Ton Spek - http//www.cryst.chem.uu.nl/pl
aton/)

• Fully automatic structure solution
• Can show students how routine service
  crystallography can function
• Give them training on a powerful tool for use in
  their research or employment.

10
Platon / System S for UNIX / Linux / FreeBSD(Ton
Spek - http//www.cryst.chem.uu.nl/platon/)

• Concentrate on the problematic - go quickly
  through the routine (transparent links to other
  programs)
• Structure Solution
• Shelxs http//shelx.uni-ac.gwdg.de/SHELX/
• Dirdif http//www-xtal.sci.kun.nl/xtal/documents/
  software/dirdif.html
• Sir http//www.ba.cnr.it/IRMEC/SirWare_main.html
• Crunch http//chemb0b.leidenuniv.nl80/rag/
• Autobuilding of structures
• EXOR, Dirdif, Sir, Crunch
• Structure Refinement
• Shelxl http//shelx.uni-ac.gwdg.de/SHELX/
• Validation, Fourier Maps, Addsym, Squeeze, etc.

11
Gretep structure plotting / symmetry (by Jean
Laugier and Bernard Bochu) (http//www.ccp14.ac.u
k/tutorial/lmgp/)

• Freely available for anyone
• Very easy to use, including
• Click and drag to rotate, translate, zoom
• Draws symmetry operators labels
• Loads common file formats - Shelx, CIF
• Includes I.D. Browns GETSPEC
• Can save all plotted information (labels, fonts,
  etc) into Gretep files

12
Gretep Showing symmetry operators (1)
13
Gretep Showing symmetry operators (2)
14
Gretep Each fragment with a different colour
15
If time limited more chance to get your points
across to students if examples are interactive
16
Scatfac for interactively investigating
scattering factors (http//www.ccp14.ac.uk/tutoria
l/lmgp/)
17
Dispano for Anomalous Scattering factor display
(http//www.ccp14.ac.uk/tutorial/lmgp/)
18
Dispano for Anomalous Scattering factor display
(http//www.ccp14.ac.uk/tutorial/lmgp/)
19
Poudrix powder pattern calculation With
Anomalous Dispersion - (Brenann and Cowan or
Sasaki)(http//www.ccp14.ac.uk/tutorial/lmgp/)
20
PowderCell powder pattern calculation (by
Werner Kraus and Gert Nolze) (http//www.ccp14.ac
.uk/tutorial/powdcell/)

• Can model multiple phases for quantitative
  analysis or modeling impurities
• Interactively modify atom occupancies and observe
  changes in the powder pattern
• Move atoms using point and click then see the
  change in the powder pattern
• Overlay a calculated powder pattern with raw
  diffraction data.
• Whole pattern unit cell refinement

21
PowderCell - interactively moving atoms (1 of 3)
(http//www.ccp14.ac.uk/tutorial/powdcell/)
22
PowderCell - interactively moving atoms (2 of 3)
(http//www.ccp14.ac.uk/tutorial/powdcell/)
23
PowderCell - interactively moving atoms (3 of 3)
(http//www.ccp14.ac.uk/tutorial/powdcell/)
24
XFIT Peak Profilingby Alan Coelho and Bob Cheary
(http//www.ccp14.ac.uk/tutorial/xfit-95/)

• Robust peak fitting
• Multiple Patterns
• No soft limit on the number of peaks that can be
  refined at once
• Can handle alpha 1/2
• Cons does not have a standard GUI interface

25
XFIT Peak Profiling - 1 of 4 Load Data
26
XFIT Peak Profiling - 2 of 4 Zoom up
27
XFIT Peak Profiling - 3 of 4 Insert Peaks
28
XFIT Peak Profiling - 4 of 4 Fit Peaks
(auto-Marquardt damping)
29
Crysfire Powder IndexingRobin Shirley
(http//www.ccp14.ac.uk/tutorial/crys/)

• Imports XFIT and other peak formats
• Links to 8 different indexing programs
• Ito, Dicvol, Treor,
• Lzon, Taup, Fjzn
• Losh, Kohl
• One line per solution summary file
• Rescaling / other features - can be indexing
  proteins from powder diffraction data

30
Chekcell GUI indexing helperLaugier Bouchu
(http//www.ccp14.ac.uk/tutorial/lmgp/)

• GUI Interface
• Reads Crysfire Summary files and XFIT peak files
• Knows about Spacegroups
• Has Le Page for reduced cell / sub super cell
  searching
• Automatic best solution
• Automatic best cell
• HKL to peak matching and optimization of
  tolerance

31
Chekcell - Systematic Absences and space group
possibilitiesLaugier Bouchu (http//www.ccp14.a
c.uk/tutorial/lmgp/)

• Scroll down through the spacegroups
• Graphically see the effects on allowed lines
• View the absence condition rules

32
Chekcell - Systematic AbsencesScrolling down the
spacegroups C2/M (1 of 5)
33
Chekcell - Systematic AbsencesScrolling down the
spacegroups P2/C (2 of 5)
34
Chekcell - Systematic AbsencesScrolling down the
spacegroups C2/C (3 of 5)
35
Chekcell - Systematic AbsencesScrolling down the
spacegroups I2/C (4 of 5)
36
Chekcell - Systematic AbsencesScrolling down the
spacegroups P21/A (5 of 5)
37
Chekcell - Systematic Absencesconditions for
P21/A within Chekcell
38
WinGX for Windows single crystal suiteLouis
Farrugia http//www.chem.gla.ac.uk/louis/softwar
e/

• Complete Single Crystal Suite for Windows
• Links to dozens of other programs (new and old)
  via GUI interfaces
• Nearly all programs are included with WinGX
  distribution

39
WinGX for Windows single crystal suite Families
of programs included/linkable with WinGX

• Importing/viewing data and models
• Absorption Correction
• Solution (Shelx, difdif, sir, patsee)
• GUI / manual shelxl97 refinement
• Hydrogen addition options
• Shelxl, GUI CalcOH, GUI XHYDEX
• Fourier Contour Map viewing
• Platon, Contour, Mapview, Marching cubes
• Structure Plotting
• Validation / publishing

40
WinGX for Windows single crystal suite
Absorption Correction

• DREAR - Blessing software
• Numerical
• Gaussian, Analytical, Spherical, Cylindrical,
  Needle
• Semi-empirical
• Psi Scans, Camel Jockey, Multiscan
• DIFABS Style
• Difabs, Xabs, Shelxa
• Interactive Visualisation of crystal faces using
  XtalView

41
WinGX for Windows single crystal suite Structure
Solution

• Shelxs97, Shels86, (Shelxd)
• Sir97, Sir 92
• Dirdif (Patterson and fragment)
• Patsee fragment searching
• SXGRAPH GUI with WinGX
• SXGRAPH Shelxl GUI allows an easy interface for
  loading of fragments for passing to Patsee or
  Dirdif

42
WinGX for Windows single crystal suite
Refinement - Shelxl 97

• GUI control of Shelx via WinGXs SXGRAPH program
• or Shelx ASCII INS File

43
WinGX for Windows single crystal suite Hydrogen
Addition options

• Shelx97 (G. Sheldrick)
• Manually edit INS file
• Via SXGRAPH GUI
• GUI XHYDEX (G Orphen)
• GUI CalcOH (M Nardelli)

44
WinGX for Windows single crystal suite Easy
Interlinking with Ton Speks Platon

• Squeeze/disordered solvent effects
• ADDSYM
• Other Platon Features

45
WinGX for Windows single crystal suite Fourier
Electron Density Contour Maps

• Use LIST 3 command in Shelxl
• Point and click map generation
• View resulting maps in
• Contour
• Mapview
• Marching Cubes by Michak Husak

46
WinGX for Windows single crystal suite Structure
Plotting

• GUI WinORTEP
• GUI WinSTRUPLO
• Platon/Pluton/ADP
• GRETEP (plugin)
• Schakal (plugin)
• Rasmol
• Photo realistic rendering
• Povray
• Render / RASTER 3D

47
WinGX for Windows single crystal suite
Validation and Structure Checking

• Platon (Addsym, etc)
• CIF Validation
• Parst
• GEOM
• THMA 14c
• IDEAL
• SYMMOL
• WTANAL
• R-tensor

48
Crystals for Windows single crystal suite David
Watkin, Richard Cooper, et al.
http//www.xtl.ox.ac.uk/

• Will focus on Guided refinement for teaching
  purposes

49
Guided structure refinement using Crystals
Import Shelx INS file of structure solved by
DIRDIF

• Asymmetric unit is always in view

50
Guided structure refinement using Crystals

• Crystals Superviser can then try and take the
  student (user) through the refinement - giving
  guidance where appropriate

51
Guided structure refinement using Crystals Have
now refined atom positions Isotropically

• The Crystals Supervisor will then make further
  recommendations
• (Crystals Scripts means custom tutorials and
  refinement logic can be added)

52
Guided structure refinement using Crystals Have
now refined atom positions anisotropically

• Atoms can be displayed anisotropically

53
Guided structure refinement using Crystals
Automatic Hydrogen Addition

• Graphically compare calculated hydrogens (white)
  to possible hydrogens found in the difference map
  (pink).

54
Interrupt the Guided Refinement in
CrystalsManual Hydrogen Addition - 1 of 2

• Crystals explains what is going on in a language
  organic chemists and students can understand (who
  may be learning single crystal methods as a tool
  for a larger project) - and displayed in organic
  chemistry text books.
• May be easier teaching crystallographic methods
  to a specialist audience starting out with their
  jargon.

55
Interrupt the Guided Refinement in Crystals
Manual Hydrogen Addition - 2 of 2

• A Wizard then guides the user to complete the
  hydrogen addition

56
Interrupt the Guided Refinement in Crystals
Generating Fourier maps and Marching Cubes for
Windows

• Easily generate Fourier contour maps to show the
  electron density. In this case electron density
  due to the missing hydrogens.

57
Guided structure refinement using Crystals
Checking Extinction

• Crystals advises and guides the user to a
  decision on whether to add extinction in as a
  parameter
• A challenge of the crystallography teaching
  course is to give the background!

58
Guided structure refinement using Crystals
Optimize weights

• Crystals advises and guides the user on how to
  optimize the weights
• Again, a challenge of the crystallography
  teaching course is to give the reasoning!

59
Guided structure refinement using Crystals
Validate Structure

• In this case validation fails and crystals
  recommends a course of action

60
Guided structure refinement using Crystals
Validation via Cambridge database geometry
checking

• To students and new users, every structure must
  seem like a new structure type. Thus using CSD
  geometry check can encourage students to look for
  errors or novel features of the structure.
• Bondlengths
• RED"too long" and BLUE"too short".
• RED ---- GREY ---- GREY ---- BLUE
• 3sigma 2sigma 1sigma 0sigma 1sigma 2sigma 3sigma

61
Validation using Crystals Cambridge database
geometry check (1 of 4)

• Doing a CSD check shows a bond in red (too long)
  displaying a geometry of which is completely
  novel in reference to what is already known

62
Validation using Crystals Cambridge database
geometry check (2 of 4)

• Using the GUI (or scripts) make the offending
  Nitrogen a Carbon and re-refine.

63
Validation using Crystals Cambridge database
geometry check (3 of 4)

• Black bonds around the renamed atom tells the
  user that the new geometry has not been tested
  against the CSD. So interrogate the CSD again to
  obtain this information.

64
Validation using Crystals Cambridge database
geometry check (4 of 4)

• CSD results now imply/infer that local geometry
  is consistent with what is already in the
  database.

65
Validation Platon for UNIX and Windows Ton
Spek http//www.cryst.chem.uu.nl/platon/

• Large range of tools including some life saving
  options.
• Will focus on Addsym for finding missing symmetry.

66
Platon Validation - Why Bother teaching this?

• For perhaps the same reason that Columbia
  University Law/Journalism professors teach their
  students (at least one - circa late
  1940s) If your mother says she loves
  you, CHECK IT OUT!!
• Encourage students to solve, refine and publish
  structures that can stand the test of time -
  that means doing a variety of validation and
  using a variety of programs to assist in
  validation!

67
Platons Addsym Structure Published in 1997 P1
- Triclinic 42 non-H atoms
68
Platons Addsym Correction Published in 1999
C2 - Monoclinic 22 non-H atoms
69
Platons Addsym Press of a button 2000 FDD2 -
Orthorhombic 11 non-H atoms(Short Communication
Abstract "P1 or P-1? Corrigendum", Acta Cryst
B56 (2000) 744 from Richard E. Marsh)
70
Bonus Personal Rant Need for the teaching of
competent computer and OS skills!

• Many universities dont seem to be teaching
  competent computer usage and programming skills.
• General computer competence now judged by the
  ability to use MS Word and Excel
• HTML taught in computer science departments as it
  was a programming language (instead of more
  difficult things like Fortran or C)
• Crystallographic teaching courses may have to
  make up for lowering standards in student
  computer competence

71
Things to consider Adding Computer skills and
Programming to teaching courses.

• If the aim is to train employable
  crystallographers consider adding one or two of
  the following to teaching courses
• Installing a dual boot UNIX (Linux/FreeBSD) and
  MS Windows PC then compiling/installing
  crystallographic toolkits as part of a medium to
  advanced crystallographic course.CCP14 based
  tutorials at
• Redhat Linux http//www.ccp14.ac.uk/solution/linu
  x/install
• FreeBSD http//www.ccp14.ac.uk/solution/bsdunix/
• Crystallographic programming as part of a
  rigorous crystallographic teaching course.
• (Most crystallographic software problems will
  probably be technical problems with the PC/?
  operating system)

72
Summary

• Advanced freely available software exists that
  can be useful for crystallographic teaching if
  intelligently applied
• This and more software is also mirrored (many
  with web based tutorials) via the EPSRC funded
  CCP14 project and website http//www.ccp14.a
  c.uk
• (3rd stage funding August 2001 to August 2006,
  London, UK)
• IUCr Xtal Nexus Software CD-ROM for laboratories
  / students isolated from the internet http//www
  .unige.ch/crystal/stxnews/nexus/index.htm (conta
  ct Lachlan Cranswick for free copy via air-mail)
• Thanks
• ACA and session chair
• Professor Dave Walker, Lamont-Doherty Earth
  Observatory of Columbia University.
• Apologies authors of other freely available
  innovative crystallographic software for the lack
  of time in not showing a few dozen more programs