CCP4 TUTORIAL PDF

Home · About CCP4 · CCP4 Projects · Downloads · Documentation · Courses · Developers · CCP4 people · WG1/WG2 · Privacy. Other MR examples can be found at the end of this tutorial, and at: When this tutorial is obtained as part of the CCP4 distribution, $MR_TUTORIAL. Previously Lecture Notes and Tutorial Material. 1、 Lecture Notes and Tutorial Material. iMosflm training · Mosflm examples. 2、 Lecture Notes and .

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Collaborative Computational Project No.

Here is tutoriak collection of tutorials starting from diffraction images. However, you need not stop at that point. In some cases the tutorials also go on to phasing and structure solution.

CCP4 Tutorial: Session 1 – Introduction

These tutorials were developed, with permission, from the X-ray Tutorial at Helmholtz-Zentrum Berlin. The second is more involved and investigates the balance between completeness and non-isomorphism when merging multiple lysozyme datasets.

Click on the headings to expand or collapse each section. Basic phasing tutorials Download tutorials and data from here: Therefore, go straight to the one which is the most interesting for you. Examples and are about Molecular Replacement, example 5 demonstrates the Crank pipeline for experimental phasing and example 6 is about the combination of the two techniques.

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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.

CCP4 Molecular Graphics – Tutorial Contents

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 ccpp4 confident enough tutrial 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.

CCP4 Tutorial: Contents

Project directories contain all necessary data for corresponding exercises. The structure contains one protein molecule in the asymmetric unit.

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. Crank pipeline for experimental phasing Automated structure solution using Crank pipeline and inflection point data.

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Structure containing several domains Location of six domains in the AU constituting two molecules of mth protein. 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.

Integration and data processing Here is a collection of tutorials starting from diffraction images. Refinement with ligands and covalent links Download and unpack tutorial data jligand.

Paths of files and cp4 will be given relative to this location.

Using links available from CCP4 dictionary Tutoril Adding glycan to a protein crystal structure and refinement of the completed structure Project directory: Using a new ligand description Description: Using a new ligand and link descriptions Description: Additional dictionary is generated defining two entries: