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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See how sensitive the autoindexing is to the main beam values. Look at the main window of the interface again, and look at the Job List. To view graphs from a log file which has not been produced by CCP4i and is hence not part of any project Job Listclick on View Any File from the menu on the right-hand side tutoriwl the main tutoriql. For the MAD data, there are 9 columns for each of 4 wavelengths. 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.

There are many ways of approaching this, and the different tools will give slightly different assessments. You can test the effect of smaller rotations than 30 degrees by:. As the images are integrated, a new window will pop up showing the average spot shape for spots near the centre of the detector, and giving the rms residual the positional error in predicting the spot positions and the weighted residual.

These are crystals of a small domain 91 vcp4 acids that have been soaked in a mercury compound. If you reply “Y”, the image will be displayed with the “bad spots” flagged with red crosses. Try changing them by mm. Often you yutorial use the output file of one job as the input file for the next cp4. Close all other windows except the main window.

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CCP4 Tutorial: Session 1 – Introduction

It may be useful to check the residual for the central region of the detector in these cases. Before starting the cell refinement, read in image 1 if it is not already displayedtuutorial Predict and make sure that the spot positions are correctly predicted.

The output file has 49 columns:. For a reasonable refinement of the parameters, the positional residual standard deviation of the spot position should be below 0.

We need to supply the spacegroup and cell dimensions, since these are not included in the input CNS file. We also need to enter an estimate of the number of residues in the asymmetric unit. First, you must start the GUI and get as far as indexing the image but you don’t need to determine the cell parameters accurately.

Predict the reflections, then use Find hkl to locate the offending reflection in the image you must give the measured indices, the first set of values in the ROGUES file, when doing this. Find the Choose module pull-down menu in the main window, and select Reflection Data Utilities. Using the search models generated by Chainsaw, we will now use Phaser to solve hypF.

The target is an acylphosphatase-like domain. Much of the information is the same as for the previous example, but there is some extra information specific to unmerged MTZ files.

We will return to Chainsaw later before running Phaser. H3 in this case.

CCP4 Tutorial – Molecular Replacement

After the job has finished, compare the plot ccp4 H32 with that of H3. This is not tutorila for unmerged data. These graphs are useful for detecting systematic absences, which can be used to identify the true space group. Therefore, go straight to the one which is the most interesting for you. The current Import job should be at the top. Select the Data reduction module, and open the Integrate Images task window.

CCP4 Tutorial – Session 1

The required ccpp4 will depend on the spot spacing to avoid mis-indexingbut in general you should know the direct beam position to within 0. Click on the headings to expand or collapse each section. You can test what completeness you would get from starting somewhere, as long as the range is within the range recommended above by the program. If you want to remove the circle, select Circles and then Erase circles from the main menu.

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This will tell you how best to collect a full data set. Read what is in the small window because you have the option of changing both the beam position and the position and size of the backstop; you only want to do the latter!

CCP4 Tutorial: Contents

This should get smaller if more than one cycle of refinement has been performed. The program will then work out the best two 15 degree segments. Integrate the 10 images again, and compare the resulting profiles with those obtained using the default value.

The target has 91 residues and a Matthews calculation strongly suggests only one molecule in the asymmetric unit. The Zoom feature has been disabled on some SGIs because it can cause the terminal to freeze. To test the higher symmetry, do the following:. The program will pause for detector parameter refinement for the centre of the image.

Another source of information is “on-line” help. In the new window give a new title such as. 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.

We are first going to convert the intensities from scalepack output to structure factor amplitudes, then from scala output to structure factor amplitudes, and discuss some statistics that are generated.