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
