Erice2008:Workshop8

From DISI

This is the detailed information for workshop #8, MAIN.

1 Aim
2 Suitability
3 Materials
4 Protocol
5 Extras

Aim

The aim of this workshop is to introduce some new MAIN functionality and its integration with PURY parameter data base. The tutorial will show how to manipulate with electron density and structure models within MAIN and how to import new structure parameters from PURY database for refinement.

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Suitability

This workshop is suitable for complete novices. Expert users are invited to bring their own data to work on. The workshop will be presented as a “hands on” format session.

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Materials

papers to read before the workshop

Turk, D. (2001) Towards Automatic Macromolecular Crystal Structure Determination. Methods in Macromolecular Crystallography. (Eds Turk. D, Johnson, L) NATO Science Series I, vol 325, ISBN: 1 58603 080 9 (IOS Press), 148-155.
Turk, D. (2007) Density modification in MAIN. V: Read, R. J. and Sussman, J. (eds.). Evolving methods for macromolecular crystallography : proceedings of the NATO Advanced Study Institute on Evolving Methods for Macromolecular Crystallography: (NATO science series, series II., vol. 254). Springer Verlag, 2007, 111-122.

websites to review before the workshop

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Protocol

Here are the step by step instructions for doing the workshop

1. First part will teach users how to import density and structural data from PDB into MAIN and perform some basic operations.
- prepare MAIN environment
- download and open structural and density data
- calculate 2FO-FC and FO-FC maps
- use kick maps
- refine

2. Second part will introduce how PURY data can be used to insert hetero molecule into structure after success with molecular replacement.
- prepare MAIN environment
- open structural and density data
- calculate 2FO-FC and FO-FC maps
- find empty density to insert ligand
- use PURY server to draw ligand and insert molecule
- create ligand - protein bond and update topology
- refine

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