Please also check the RapiData2012 autoPROC Wiki!
Please check here from time to time - we'll update it during the course as we go along! Come and ask us (Claus & Clemens) if you have any questions.
Content:
Introduction
Please check from time to time this page - we try to keep it up-to-date.
All necessary files for these tutorials should be available for download on the various tutorial pages themselves.
It should be enough to type
% sharp
on any of the workshop computers (and read the message printed to the terminal). Or go directly to http://localhost:8080/ and login.
Background:
- C. Vonrhein, C. Flensburg, P. Keller, A. Sharff, O. Smart, W. Paciorek, T. Womack and G. Bricogne (2011). Data processing and analysis with the autoPROC toolbox. Acta Cryst. D67, 293-302
- M. Schiltz and G. Bricogne (2010). `Broken symmetries' in macromolecular crystallography: phasing from unmerged data. Acta Cryst. D66, 447-457.
- Clemens Vonrhein, Eric Blanc, Pietro Roversi and Gérard Bricogne (2007). Automated Structure Solution With autoSHARP. Methods in Molecular Biology 364, 215-230.
- G. Bricogne, C. Vonrhein, C. Flensburg, M. Schiltz and W. Paciorek (2003). Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Cryst. D59, 2023-2030
Data provided for 'playing' by organisers
The organisers of the workshop will provide some data for 'playing' - especially useful during the start of the workshop when no new data has yet been collected.
Available are
- c3_x29 (Se-MET data) work in progress
- ly49bp-4 (S-SAD phasing) work in progress
Processed data (from autoPROC) can be found in
/img03/data1/pxuser/RD2012/play/autoPROC
/img06/data1/pxuser/RD2012/play/autoPROC
Se-MET peak 1o22
A tutorial on 1O22 from JCSG is available here. It uses the same data that was part of the autoPROC tutorial.
Existing tutorials
Own data
To work with your own data in SHARP/autoSHARP, please have the following available (for details see autoSHARP documentation):
- reflection files:
- *.sca files (merged SCALEPACK format with I+ and I- measurements - unless native data for SIR/MIR)
- *.mtz files (merged files containing DANO/SIGDANO columns in case of anomalous data)
- sequence:
- *.pir sequence file in correct format
- atomic model:
- model*.pdb file with final model (for comparison) and/or partial model (to use this for heavy atom detection in autoSHARP)
- heavy atom information:
- *.hatom file with (fractional) coordinates of known heavy atom positions
Apart from obviously reflection data, all other data files are optional. If you don't have a sequence file handy, you can use the number of residues (1 amino-acid is about 110 Da) instead.