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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Look for a gap of around e. When setting up the cell refinement, when asked “Use the current orientation” tutoeial “no” and then supply the name of the appropriate matrix file. Rejecting a significant number of the strongest reflections can give problems in structure solution.

Extra information is now displayed at the bottom of the display window.

CCP4 Molecular Graphics – Tutorial Contents

At the bottom of the display, the first 10 reflections are listed more can be listed via the List More Info option:. This is a different structure of the same protein as 1v3z.

This protein has a Hg derivative. Note however that the positional residual will be higher for weak data, as the spot positions are not as well defined.

The simplest way to do this is through CCP4i. For answers to problems not resolved by these sources, feel free to e-mail Harry Powell. 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.

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Click on Circles in the Main menu to display resolution circles. If there is clearly a trend that the mosaic spread is changing with phi it can increase due to radiation damage or change because it is anisotropic then you can either make the program use the refined value:. The success of autoindexing is critically dependent on the accuracy of the direct beam coordinates.

Refinement with ligands and covalent links Download and unpack tutorial data jligand.

Look at the predictions of the reflections on the image. Beware of using more than 3 segments; futorial calculation can take a very long time and you gain very little! Much of the information is the same as for the previous example, but there is some extra information specific to unmerged MTZ files.

CCP4 Tutorials

Check against cpc4 contents of the PDB file why they should have such a value. Normally you will want to reset the misseting angles to those of the first image, because you will start integration with that image. The Zoom feature has been disabled on some SGIs because it can cause the terminal to freeze.

The names of these columns are given here. This will happen if you have rather weak images no strong spots in the outer regions of the detector. Leave the next line as:. In this exercise, we examine an unmerged MTZ file. Graphs can be edited and annotated, and printed either to a PostScript file or directly to a printer.

CCP4 Tutorial: Contents

This is not appropriate for unmerged data. If not, then the autoindexing has failed check the direct beam coordinates, wavelength, detector distance. In some cases the tutorials also go on to phasing and structure solution.

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Errors in the initial cell may give different values, especially if more than one segment is being used. The refined detector distance may also differ for images in different segments at the start of refinement compensating for errors in cell parameters. Graphs are selected by first clicking in the middle window to select a group of graphs, and then clicking in the bottom window to select a particular graph.

CCP4 Tutorial – Session 2

In the MTZ format, the column names are not fixed, and neither is the order of the columns. 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. The program will then come up with 2 segments of 15 degrees to get the most complete data possible. Click on List More Info at the bottom of the display window. 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.

Enter this value via “Processing params” panel and repeat the prediction to see if it looks better.