Phasing using CCP4

Download tutorials and data from here: ccp4_phasing.tgz

It's not likely that you will be able to go through all these exercises in two hours. Therefore, go straight to the one, which is the most interesting for you. Examples 1-4 and 6-8 are about Molecular Replacement, example 5 demonstrates the Crank pipeline for experimental phasing and example 6 is about the combination of the two techniques. Example 4 illustrates the fitting of a model into electron density maps in the context of MR structure solution, but the same technique may be used for experimental phases.

Exercise 1 is an introduction to the MR programs in CCP4 and to the CCP4I interface. Exercise 4 uses Molrep and requires some bookkeeping, but is a useful step-by-step procedure and will allow you to see changes in the maps as the structure solution progresses. Exercises 2, 3 and 6 are from the Phaser web-site and are probably the most important ones although not very difficult with the modern version of Phaser. If you are confident enough with Molrep or Phaser, try example 7 - it may not be entirely straightforward and its description does not contain step-by-step instructions. Example 8 illustrates a frequent problem with the space group assignment in the presence of pseudo-symmetry and twinning and how an incorrect assignment may affect MR structure solution. Example 5 contains step by step instructions on how to use the Crank pipeline in the default mode for experimental phasing.

It is recommended to set up a new ccp4i project for each of the examples and set the project directory as indicated below. Project directories contain all necessary data for corresponding exercises. They are located in the directory ccp4_phasing which can be downloaded from the above link.

1. Introduction to CCP4 programs for MR

Solution of hypF structure using Molrep, Phaser or MrBUMP.
The structure contains one protein molecule in the asymmetric unit.
Project directory:      1_intro
Details

2. BETA/BLIP (a protein-protein complex)

Solution of Beta-lactamase:BLIP complex using Phaser
Project directory:      2_complex
Details

3. TOXD (using ensemble models)

TOXD structure solution with ensembles in Phaser.
Project directory:      3_ensemble
Details

4. Using Phased RF and TF

Positioning the large and small domains of sucrose-phosphatase using conventional Patterson search and search in electron density map, respectively.
Project directory:      4_saptf
Details

5. Crank pipeline for experimental phasing

Automated structure solution using Crank pipeline and inflection point data.
Project directory:      5_crank_infl
Details

6. Combined MR-SAD

MR-SAD tutorial with S-SAD lysozyme and goat alpha-lactalbumin as model
Project directory:      6_mr_sad
Details

7. Structure containing several domains

Location of six domains in the AU constituting two molecules of mth685 protein.
Project directory:      7_domains
Details

8. Revising point group assignment

Twinning interfering with pseudosymmetry as well as low data quality make it possible to "solve" this structure in an incorrect orthorhombic space group.  The procedures that led to both false and true solutions are demonstrated including symmetry assignment and data merging.
Project directory:      8_symm
Details

More MX tutorials

EPS-CCP4 school
http://www.ccp4.ac.uk/schools/APS-school/index.php

Phaser tutorials
http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials

Tutorials on Helmholtz Zentrum Berlin website
http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/tutorial/index_en.html

Tutorials distributed with CCP4
$CCP4/examples/tutorial/html/index.html
$CCP4/mr_tutorial_2006/mr_tutorial_first.html (example 1 in this collection)
$CCP4/examples/mr_tutorial_2006/mr_tutorial_advanced.html

Molrep tutorial
http://www.ysbl.york.ac.uk/~alexei/downloads/tutorial_MR.tar.gz