Kyoto-2008 Crystallographic Computing School

Introductory Talk Ton Spek, Kyoto, 18-08-2008

WELCOME

Irasshaimase!

• Introductory Talk, History

Ton Spek

• Overview of the Scientific Program

Ralf Grosse-Kunstleve

• Practical Details,

Min Yao

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 60’s, 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).

16kW Operator Plotter Output Input Console ~1966, Electrologica X8 ALGOL60 ‘Mainframe’ (<1MHz)

Flexowriter for the creation and editing of programs and data

Direct Methods Meetings

• Many meetings and schools in the 70’s 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 :

1978 Erice School Direct Methods

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• MULTAN was eventually superseded in the 80’s by the even more powerful SHELXS, SIR & DIRDIF software.

• In the 90’s S&B, SHELXD coming down from Macro-crystallography.

• Mainframe  entered the field, Lab Mini (MicroVAX)  PC/WS

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)).

SHELX76-STYLE FORTRAN

Current Hardware Platforms

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

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: GUI’s, Data collection & Data Reduction, Databases, Validation, Automation.

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 

Computing School Siena 2005

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

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.

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

Thanks to our Sponsors !

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