Kyoto2008 Crystallographic Computing School

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Kyoto-2008Crystallographic Computing School

• Introductory Talk

Ton Spek, Kyoto, 18-08-2008
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WELCOMEIrasshaimase!

• Introductory Talk, History
• Ton Spek
• Overview of the Scientific Program
• Ralf Grosse-Kunstleve
• Practical Details,
• Min Yao

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Some History

• Many of the older software developers, like me,
  have a background in Direct Methods for solving
  the phase problem that is today essentially
  solved.
• I started in the mid 60s, more than 40 years
  ago, at Utrecht University in the Netherlands as
  a small molecule crystallographer.
• At that time, I had to write my own Direct
  Methods program in the ALGOL-60 language in order
  to solve my structure.
• The next slide shows a university mainframe at
  that time (essentially single user, FG/BG).

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16kW
Operator
Input
Plotter
Output
Console
1966, Electrologica X8 ALGOL60 Mainframe
(lt1MHz)
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Flexowriter for the creation and editing of
programs and data
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Direct Methods Meetings

• Many meetings and schools in the 70s were
  organized with Direct Methods (software and
  theory) to solve the phase problem as the central
  theme.
• Inspiring were the CECAM Direct Methods workshops
  in Orsay (France) bringing together experts in
  the field to work on current issues for 5 weeks !
  around an for that time big European IBM-360 with
  lectures by Herbert Hauptman.
• Famous were the schools in Parma, York Erice.
• Photo of the participants of the 1978 Erice
  School next

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1978 Erice School Direct Methods
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Tools and Platforms Changed

• MULTAN from the York group came out as the
  standard phase solution program for 15 years.
• Multiuser Mainframes, FORTRAN and PUNCHCARDS
  became the standard platform.
• MULTAN was eventually superseded in the 80s by
  the even more powerful SHELXS, SIR DIRDIF
  software.
• In the 90s SB, SHELXD entered the field, coming
  down from Macro-crystallography.
• Mainframe ? Lab Mini (MicroVAX) ? PC/WS

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Software Languages

• Crystallographic software has been written in
  machine language, assembly language, algol60,
  (turbo)basic, (turbo)pascal, Fortran, C, C and
  various scripting languages such as python
• Stone-age Fortran based software is still
  ubiquitous in the small-molecule world (ORTEP,
  SHELX, CRYSTALS, SIR, DIRDIF, PLATON etc.)
• New (commercial) software development mainly in
  C and scripting languages.
• A project in the UK aims at a rewrite and
  documentation old Fortran based software to C
  (Durham, Oxford Age-problem project (David
  Watkin)).

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SHELX76-STYLE FORTRAN
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Current Hardware Platforms

• MS-Windows (PC)
• Small-Molecule Crystallography
• Powder crystallography
• UNIX/LINUX/OSX (PC or Cluster)
• Macro Crystallography
• (Small-Molecule Crystallography)

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Current Computing Areas

• Bio-crystallography Phasing, Building,
  Refinement, Graphics etc.
• Chemical Crystallography Powder Diffraction,
  Charge Density Studies, Incommensurate
  Structures, Diffuse Scattering, Structure
  Analysis,Charge Flipping.
• General GUIs, Data collection Data Reduction,
  Databases, Validation, Automation.

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IUCr Computing Schools

• .. Mostly held jointly with IUCr Assemblies
  Examples
• 195? - Pepinski
• 1963 - Rollett, Algorithms (black book)
• 1969 - Least-Squares Absorption Correction
  (SHELX76 - code)
• 1978 - Program systems (SHELX, XTAL, NRCVAX etc.)
• 1996 - Macro-crystallography
• 1999 - Macro-crystallography
• 2005 - Siena (Small, Macro)
• Photo of Siena (It) school next ?

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Computing School Siena 2005
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Outcome of Siena-2005

• The Siena lectures have been archived in the
  Sept-2005 Newsletter of the computing commission
• http//www.iucr.org/iucr-top/comm/ccom/newsletters
  /2005sep/iucrcompcomm_sep2005.pdf
• Paper on the Hooft parameter based on discussions
  in Siena
• Hooft et al. (2008). J. Appl. Cryst.,41, 96-103

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Motivation for this Crystallographic Computing
School

• A general feeling within the small-molecule
  community is The current generation of software
  developers is phasing out. Where is the new
  generation to keep things running in the future
• There exists a growing community of push-button
  users using Black Box and Proprietary Software
• - What is not behind a button can not be
  done
• - Lack of info about the algorithms used
• A new generation of crystallographers should be
  trained to maintain, modify and develop Open
  Source software to secure continuity and
  scientific advance.

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Issues to Consider

• A large FORTRAN code legacy
• Evolutionary Update of Current Software or Start
  from Scratch
• Documentation of currently Implemented Algorithms
• Toolboxes
• Funding of Software maintenance and development

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Thanks to our Sponsors !

• Bruker-Nonius AXS
• Cambridge Crystallographic Data Center
• CCP4
• Hokkaido Wako
• IUCr-Osaka
• Infocom
• NTC
• Oxford Diffraction
• Phenix
• Rigaku
• Sgi-Japan

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