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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This model should be submitted to 20 cycles of automated refinement, then checked manually against 2mFo-DFc and mFo-DFc maps, using a graphics program such as Coot. See how much the cell parameters change.

The required accuracy will depend on the spot spacing to avoid mis-indexingbut in general you should know the direct beam position to within 0. In this exercise, we examine an unmerged MTZ file.

Fractional bias may tutroial an indication of “Partial bias”. If the peak region is too big i. However, this depends on the software being correctly installed at the beamline, and the necessary communication between the program controlling data collection and the MAR software, and this is not always reliable.

CCP4 Tutorial – Session 2

Tutlrial indicates the “noisiness” of the profile it is the variation in the background after scaling the peak to It does not matter if they change slowly and by an amount per images that is less than 0. For orthorhombic or lower symmetries, the use of two or more images will give better estimates of the cell parameters, and this is recommended.

By default all found spots from all images will be used in autoindexing, but any gutorial of images can be selected using Select images. The names of these columns are given here. Click on the grey title bar of the folder and enter:. The final sd in spot positions should be one pixel or less.

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We also need to enter an estimate of the number of residues in tutorlal asymmetric unit. By default, only the header information from the MTZ file is displayed.

This is not appropriate for unmerged data.

Now we can revisit the anomalous Patterson. We will return to Chainsaw later before running Phaser. In the case, the default format statement is slightly wrong, and needs to be changed to:. A negative partial bias will result if the mosaic spread is underestimated, or if there is a lot of diffuse scatter. In the following instructions, when you need to type something, or click on something, it will be shown in red. The structure contains one protein molecule in the asymmetric unit.

The graphs in Acentric Moments of Type the input into the control window which comes up when you click on Strategy from the Main menu. Find out the centre and extent of the backstop shadow using the left mouse button and looking at XC and YC in the Output panel.

These plots confirm there is no problem with twinning. This example will take the output from step 2a. In the main display window, the batch header for each batch is displayed.

The ROGUES file gives you the image Batch on which the reflections have been recorded for partials, this is the image nearest the centre of the reflection, so you may need to look on the preceeding and following image as well. Each column has an associated type. Check the variation in B-factor with image B v rangeand if there is no real variation less than 2 or 3 units, either positive or negative it is best to turn off the B-factor refinement. Such pixels are excluded from the integration.

Gives some useful statistics as a function of resolution.

The so called “cumulative intensity statistics” tabulated by TRUNCATE and plotted by LOGGRAPH provides the only point at which you will be able to detect merohedral twinning when the two lattices of the twin components exactly overlap, and every measured intensity is actually the sum of two intensities. Change the Max value in the image display window to and zoom an outer part of the image to get a better idea of the quality of the image.

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Those reflections which appear on the image near the rotation axis cannot be measured accurately by any method the student is encouraged to become familiar with the Ewald Sphere construction which explains why this is so.

CCP4 Tutorial: Contents

These will be dealt with below, so click Dismiss. Output from the programs or text from the tutoriql is given in green. H3 in this case. To do this, in the Temperature Factor Analysis task window, click on the View button in the line where the PDB file was selected – this will display a CCP4i fileviewer window with the contents of toxd. Please note that you can alter the cdp4 of the loggraph window by using the Appearance, Edit and Utilities facilities provided e.

Molrep tutorial Alexei Vagin. You have already completed the native set, cc4p the MAD measurements extend to a lower resolution. You should find that this is more difficult! When the refinement has finished, image 1 will be displayed with NO spots predicted and the message “Waiting for input” will appear over the image, and a summary of the refinement will be given in an output window:.

CCP4 Tutorial: Session 1 – Introduction

The second is more involved and investigates the balance between completeness and non-isomorphism when merging multiple lysozyme datasets. Investigate this in the exercise below.

This depends on the mosaic spread and minimum separation. After the ten images have been displayed select Continue to step throughthe program will form the standard profiles in this example, 24 different profiles for different areas of the detector and integrate the images