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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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CCP4 Tutorials

There is native data in H32 to 1. Remember to check adjacent images for partials. The program will now integrate these images, and use the resulting tutofial to refine the cell parameters, crystal orientation and mosaic spread using the post-refinement procedure.

This region of the detector is therefore called the “blind region”; because of its appearance in the image, it often also called the “bow-tie”, “apple-core” or “cusp” region. Type the input into the control window which comes up when you click on Strategy from the Main menu.

Using a new ligand description Description: The output file has 49 columns:. The shape of the symbol depends on the terminal program you are running – it could be a rectangle seen on Unixa letter seen on Linuxor a Windows symbol. To enter a new value for any of these, just click on the appropriate parameter, enter the value and hit Enter. The final sd in spot positions should be one pixel or less. Please note that you can alter the layout of the loggraph window by using the Appearance, Edit and Utilities facilities provided e.

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. This uses a cardiotoxin 1tgx.

Graphs can be edited and annotated, and printed either to a PostScript file or directly to a printer. The output file should be automatically set to:.

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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 This will happen if you have rather weak images no strong spots in the outer regions of the detector.

Select Refine cell Main menu and use one segment of 2 or 3 images for orthorhombic or lower symmetries you should use 2 or 3 segments with images widely separated in phi.

Reflection records are grouped into batches: You tuutorial now prepared three search models based on 1v3z, and used Molrep and Phaser to do the molecular replacement. If you reply “Y”, the image will be displayed with the “bad spots” flagged with red crosses. Pixel values are represented by numbers and then letters A-Z. As established abovebatch number 74 is a rather serious outlier.

Information about the datasets included in the file is given here. Gives some useful statistics as a function of resolution. Run as above, with the following differences:.

CCP4 Tutorial: Session 2 – Data Processing and Reduction

This can happen if the mosaic spread is too small, so that these reflections are actually partials. Fractional bias may show tutoial indication of “Partial bias”. Then do for example:. Try changing them by mm. 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 former in this case!

In this example, the file just contains one dataset. In the MTZ format, the column names are not fixed, and neither is the order of the columns.

CCP4 Workshop: Lecture Notes and Tutorial Material

We will do the scaling in spacegroup H3, look at the output, look at excluding ‘rogue’ images from scaling, check statistics tabulated by program TRUNCATE and investigate the true spacegroup H3 or H32? If you want to remove the circle, select Circles and then Erase circles from the main menu. In this example, we will combine the native data we have just processed with some MAD data for a selenomethionine derivative of GerE.

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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 of the main window. Here “SdFac” is an overall scale factor, and “SdAdd” is an intensity dependent factor.

Many images can be used in the autoindexing although there is a limit of spots. These steps, and the initial discovery of 1v3z and other related proteins, are automated in the program MrBUMP.

Using a higher value for the mosaic spread tutogial result in more boxes being overlaid, and some of the blue boxes will change to yellow. Look for the following:. 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:.

Close or Quit thtorial other interface windows except the main window. Example 5 contains step by step instructions on how to use the Crank pipeline in the default mode for experimental phasing. You should now be in a position to process your own data.

CCP4 Molecular Graphics – Tutorial Contents

It is considered good practice to add in all vcp4 reflections appropriate to the spacegroup and resolution, even if there is no data for them “completing the dataset” and to add a column of free-R flags at this stage to the master dataset. Compare the plotted tutoriwl of the moments with the Expected values shown at the top of the window. Is this the case for this data?

The use of a few local PDB template files also means that the tutorial is fairly quick. Leave the next line as:. This depends on the mosaic spread and minimum separation.