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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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. Check how the mosaic spread is changing. In such cases you should check that tutoriql supplied the correct beam coordinates, to avoid the risk of mis-indexing the image.

CCP4 Tutorial: Molecular Replacement

At this stage, we can have a look at the anomalous Patterson for these data. If it is above 0. The use of a few local PDB template files also means that the tutorial is fairly quick. Finally you are given the option of selecting the solution default yes. Check against the contents of the PDB file why they should have such a value. Such pixels are excluded from the integration. These steps, and the initial discovery of 1v3z and other related proteins, are automated in the program MrBUMP.

Extra information is now displayed at the bottom of the display window. If you have done more than one integration run during your MOSFLM session, you will find multiple entries of the tables. It is possible to save the current values of the detector, beam and crystal parameters to a file, which can be executed by typing filename to restore these values if something goes badly wrong or if the program crashes should never happen of course!

However, if you do not have the output file, then it will also be available in directory DATA.

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CCP4 Molecular Graphics – Tutorial Contents

In the File completion and freeR extension folder, make sure the radio button is off. A list of batches is given at the end of the default display:. 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. 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.

Click on the ccp to expand or collapse each section. This table also shows shell and cumulative R-factors. We will return to Chainsaw cdp4 before running Phaser.

If you want the complete list of possibilities again, give the reply N to the following question the second question that is asked when running the autoindexing:. If the peak region is too big i.

CCP4 Tutorial – Session 2

We will see later that all but the 0,0,0 peak are symmetry equivalents. If you do exit, follow the instructions at the end of this section on how to restart from saved parameters. Have a look at these graphs. 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.

Additional dictionary is generated defining two entries: Basic phasing tutorials Download tutorials and data from here: For answers to problems not resolved by these sources, feel free to e-mail Harry Powell. If some data have already been collected: Note the value for mosaic spread in the text window giving the refinement. The window will be closed automatically when the task has been finished. Fractional bias may show an indication of “Partial bias”.

In the early stages of data processing, however, one has several observations of each reflection i. This will open a Task window. In the new window give a new title such as. Try reading in fcp4 image, run Find spots and Autoindex again.

For orthorhombic or lower symmetries, the use of two or more images will give better estimates of the cell parameters, and this is recommended. In this example, all columns belong to dataset 1. The shape of the symbol depends on the terminal program you are running – it could be a rectangle seen on Unixtutoorial letter seen on Linuxor a Cc;4 symbol. By default, only the header information from the MTZ file is displayed. 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.

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We will do the scaling in spacegroup H3, look at the output, look at tugorial ‘rogue’ images from scaling, check statistics tabulated by program TRUNCATE and investigate the true spacegroup H3 or H32?

Please note that you can alter the layout of the loggraph window by using the Appearance, Edit and Utilities facilities provided e. To test the higher symmetry, do the following:. H3 in this case.

The data are from the crystal structure of GerE, a transcription activator from Bacillus subtiliswhich was solved by MAD phasing using the Se signal V. If you reply “Y”, the image will be displayed with the “bad spots” flagged with red crosses.

The program will now integrate these images, and use the tuorial intensities to refine the cell parameters, crystal orientation and mosaic spread using the post-refinement procedure. Often you will use the output file of one job as the input file for the next job.

Try changing them by mm. Close or Quit all other interface windows except the main window. The file contains 6 columns; 3 holding the hkl indices, and 3 containing data. Alternatively, get the images directly from http: Enter this value via “Processing params” panel and repeat the prediction to see if it looks better.

You can exclude a given batch from the scaling.