Kyoto-2008Crystallographic Computing School

Introductory Talk

Ton Spek, Kyoto, 18-08-2008

WELCOMEIrasshaimase!

• 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).

~1966, Electrologica X8 ALGOL60 ‘Mainframe’ (<1MHz)

16kWOperator

InputOutputPlotter

Console

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• MULTAN was eventually superseded in the 80’s by the even more powerful SHELXS, SIR & DIRDIF software.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 entered the field, coming down from Macro-crystallography.

• Mainframe 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