The University, St' Andrews

1
Introduction to CCP4

• Jim Naismith
• St. Andrews University
• CCP4 BBSRC SUMMER SCHOOL
• 23rd-27th August 1999

2
What is CCP4?

• Collaborative Computing Project No. 4
• Web page
• It administers the package of software known CCP4
• Funded by the BBSRC to research new methods in
  structure determination

3
Who is CCP4?

• Working Group 1 Heads of lab from around the
  U.K. (Industry and academic, one per
  University/company)
• Policy made by WG1, (exec group)
• Working Group 2 Software bods from UK labs
• Software implemented by WG2

4
CCP4 staff

• Day to day running is done by Sue Bailey
• Day to Day policy is a done by Exec committee
  (Isaacs (chair), Naismith, Dodson, Evans, Bailey,
  Harding (BBSRC)) subject to WG1 approval
• Programmers Alun Ashton, Liz Potterton, Martin
  Winn, Peter Briggs

5
How big is CCP4?

• Industrial laboratories renew their license each
  year for a donation (approx 600)
• Academic labs get everything for free for ever
• Currently 481 academic labs licensed and 85
  Industrial labs licensed
• runs on all unix based operating systems

6
What is the package?

• Collection of programs donated by high minded
  individuals
• The essence of the suite is the fact that they
  operate a common set of interfacing routines and
  data structures
• This modular approach allows new functionality to
  be incorporated quickly
• Interfacing through the command script

7
What sort of things does it do?

• Merges data (integration is carried out by
  MOSFLM, linked to CCP4)
• Calculates cell density, chops around PDB files
• Calculates phases (solving structures by MAD,
  MIR, SIR and Mol repl)
• Calculates maps (of all descriptions)
• Analyses and refines structures

8
What it does not do

• No map fitting software to speak off
• Does not run CNS and DENZO, these all rely on
  text input, separate programs
• (provides good conversion programs to convert
  format of files)
• Does not collect data

9
MTZ file

• The reflection file format. It is a binary file
  but on unix you can tail an mtz file and read the
  header
• Inside an mtz is a spreadsheet.
• The headers are H,K,L, User1,User20
• User are things we want to store, F, SIGF, Phase
• viewed by mtzdump

10
CCP4 command script

• /bin/csh -f
• setenv VARIABLE value
• ccp4 HKLIN myin.mtz HKLOUT myout.mtz ltlt x
• KEYWORD value
• KEYWORD value
• x

11
Running a command script

• ccp4.com gt ccp4.log
• This runs the program and put the output into a
  log file. In the log file is a record of what the
  program did. Can be view graphically

12
Advice on running the scripts

• Have a text window open to do the editing
• Have a netscape window open along side, set to
  program web page
• Steal some elses command script or use an example
• Worry about what you do, not how you do
• If a value sounds obscure, the default is
  probably OK (ie BESLIM, rholim)