CCP4 TUTORIAL PDF

See also the accompanying document giving background information. In the following instructions, when you need to type something, or click on something, it will be shown in red. Output from the programs or text from the interface is given in green. First, we scale each derivative to the native dataset, so that all data is on the same scale. At the same time, we analyse the heavy atom data to estimate the strength of the signals.

Author:Akinole Zulkijin
Country:Botswana
Language:English (Spanish)
Genre:Automotive
Published (Last):22 February 2015
Pages:304
PDF File Size:6.58 Mb
ePub File Size:1.90 Mb
ISBN:720-4-18388-314-3
Downloads:13776
Price:Free* [*Free Regsitration Required]
Uploader:Arashigrel



See also the accompanying document giving background information. This is an introduction to the procedures for using Refmac5 to refine a crystal structure.

See also the documentation for Refmac5 and Sketcher. In the following instructions, when you need to type something, or click on something, it will be shown in red.

Output from the programs or text from the interface is given in green. This example is to refine the protein RNAse Sa in its unliganded and liganded form, for which we know:. The final structure solved by Joseph Sevcik: J. Sevcik, Z. Dauter, V. Lamzin, K. Wilson, Acta Cryst. D52 p looks like this:. There are atoms in the asymmetric unit. If we describe each atom using three positional parameters x,y,z and an isotropic temperature factor B there are parameters.

This is not enough to refine all parameters as independent variables. However we have a great deal of information about the geometry of molecules - the bond lengths and bond angles etc. The refinement program will set up restraints between related atoms which say, for example, that the distance between two bonded atoms must be close to the ideal bond length. Refinement programs read libraries describing the expected geometry.

These contain information about the ideal bond lengths, bond angles, planar groups etc. If this information is incorrect you will not get a correct structure. If your structure contains an unusual substrate molecule or a modified amino acid, then there may be no suitable description in the library, and you will have to provide one in the required style. This can be difficult; it is essential you know the chemical definition of your ligand, e.

This knowledge must then be written in the correct format for the refinement program to read. This can also be challenging, so we will make the geometry description for the ligand to show how it is done.

Also, all residues have been shifted by up to 0. The program will look at the atom coordinates and decide where there are disulphide bonds, cis-peptides and D-peptides. It will also calculate the distance between atoms and if they are very close it will assume the atoms are bonded and will make a make a restraint to say 'these two atoms must stay close'. Of course this is not always right. It will also add any absent atoms - if a residue does not have the right atoms it will make them.

From the Refinement module select Run Refmac5. Look in the folder called Setup Geometric Restraints. In here you can decide what to look for in the PDB file. We will use the defaults - you do not need to change anything. From the Run menu at the bottom of the window choose Run Now. The job will take a little time. Look at the log file click on the name of the job, refmac5 , in the main window and use View Files from Job and View Log Files. These things are correct, REFMAC5 has checked the input protein molecule and found some cis peptide bonds and some disulphide bonds, but there is also:.

It is necessary to edit the PDB file to remove the bad link information. There is an easy way to do this. The space group and the symmetry operators for the space group you may need this information to define disulphide bonds or links between molecules that are not in the same asymmetric unit.

LINK definitions describe ways to link two monomers, e. This is a way to redefine non-standard residues. Do this three times. When it is finished look at the log file click on the name of the job, refmac5 , in the main window and use View Files from Job and View Log Graphs.

You will see a graph of the R factor and the Free R factor for the 6 cycles of refinement. The R factor is very good already but both go down a little. The FOM tells you how well the molecule matches the experimental data and the Geometry tells you how well the molecule obeys the geometry restraints.

The red line is the average R factor versus resolution for the data which is used and the green line is the Free R factor for the 'free' data which is not used.

This is similar across the resolution ranges - it does not go up for high resolution data. This is an example of what is good about maximum likelihood refinement compared with the old-fashioned least squares.

This is a graph of the average observed structure factors and calculated structure factors. You notice that at low resolution the observed red and the calculated blue are not the same. At low resolution the water atoms, which we can not see in the crystal structure, are an important part of the structure factors.

The refinement program tries to model the water atoms by solvent scaling but it is difficult for this data because some of the very low resolution data is missing. To close the loggraph window click on the File menu and select Exit. In the file you will see:. An example of these maps is shown below for a tyrosine residue which is in the wrong place. Here you can see a large pink area of negative density where the tyrosine side chain is now.

This is saying that the side chain should not be here. The large brown-red area of positive density is showing where the side chain should be.

From the Refinement module select the Monomer Library Sketcher task. You will see the molecule displayed. You can rotate it by holding down the left mouse button. On the right of the window is a list of atoms - this list has the element, the atom name and the oxidation state the charge of the atom. Below the list of atoms is a list of the chiral centres found in the molecule, of which there are four. Now look at the monomer library file.

The refinement program will try to make the ligand as defined in this file - you can edit the file if you need to. If you already have sketcher open from the previous exercise, delete any molecule that you have displayed: from the Edit pull down menu select Delete All Atoms. Select the file:. The picture of GMP below shows the correct delocalised and aromatic bonds - edit your molecule accordingly. To change a bond to a delocalised bond, you must hold down the Shift key on the keyboard and click on the bond with the right mouse button.

It will step through single--double--triple--deloc--aromatic--metal. Now create the monomer library. From the File pull-down menu at the top of the window select Create Library Description. Then enter the name of the ligand this must be GMP which is the name of the ligand in the PDB file which we will refine. Then Close this window. When it has finished the molecule is displayed again. Now look at the new monomer library file. From the Main Window select the last job which is called dictionary.

This list is not quite the same as for the monomer 3GP as it is in the Monomer Library. Have a look at the differences and update as you see fit. This section is optional. Alternatively you can go directly to the next step - Review Special Restraints for ligand.

If you have no coordinates or other definition of the ligand then you must draw the molecule in the Sketcher. Sometimes there may be a similar molecule in the library - you can start from this and edit it. Delete any molecule that you have displayed: from the Edit pull down menu select Delete All Atoms. In the new window, from the folder Choose Monomer, select:. You must wait a little while before the molecule of guanosine is displayed.

From the edit tools on the left of the Sketcher window select the 'Delete atom' icon from the edit tools on the left of the window. To add the new phosphate group select the the 'Add a C atom' icon from the edit tools. The atoms that you add will be carbon atoms - you will change them later to phosphorus and oxygen. Now look at the end of the table on the right side of the Sketcher window. Change C21 to a P and the other three to O.

The bonds within the phosphate are delocalised bonds, so click Shift - right mouse button on the bonds between P and all three O atoms, stepping through the bonds until they are 'deloc' bonds. Now we create the monomer library. Close this window. Wait while the program runs to build the dictionary file. The molecule is drawn again. If necessary you can make corrections and run again.

FUNCTIONAL ANALYSIS M THAMBAN NAIR PDF

CCP4 Tutorial: Session 1 - Introduction

See also the accompanying document giving background information. In the following instructions, when you need to type something, or click on something, it will be shown in red. Output from the programs or text from the interface is given in green. MOSFLM can process diffraction images from a wide range of detectors and produces, as output, an MTZ file of reflection indices with their intensities and standard deviations.

FANUC A06B-6132-H002 PDF

CCP4 Tutorial: Session 3 - Heavy Atom Search and Phasing by MIR

See also the accompanying document giving background information. In the following instructions, when you need to type something, or click on something, it will be shown in red. Output from the programs or text from the interface is given in green. First, we scale each wavelength of the MAD data to the native dataset, so that all data is on the same scale. At the same time, we analyse the MAD data to estimate the strength of the dispersive and anomalous signals. Now select the columns from the MTZ file. Then select columns for the 4 wavelengths, using the button Add Derivative Data to add more columns.

HISTORIA DE LA IGLESIA PRIMITIVA - HARRY R.BOER PDF

CCP4 Tutorial: Contents

See also the accompanying document giving background information. In the following instructions, when you need to type something, or click on something, it will be shown in red. Output from the programs or text from the interface is given in green. If you have problems following the instructions, then you can use. Often you will use the output file of one job as the input file for the next job. However, if you do not have the output file, then it will also be available in directory DATA. When using ccp4i for the first time, you need to set up a project to work in.

EL EVANGELIO DE QUETZALCOATL PDF

CCP4 Tutorial: Session 2 - Data Processing and Reduction

See also the accompanying document giving background information. This is an introduction to the procedures for using Refmac5 to refine a crystal structure. See also the documentation for Refmac5 and Sketcher. In the following instructions, when you need to type something, or click on something, it will be shown in red.

Related Articles