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 at the main window of the interface again, and look at the Job List.
CCP4 Tutorial: Session 1 – Introduction
Exercise 4 uses Molrep and requires some bookkeeping, but is a useful step-by-step procedure and will allow you to see changes in the maps as the structure solution progresses. This procedure will output a file of structure factor amplitudes and intensities for the reflections that were collected.
The output PDB file uses the naming and numbering of the target sequence. The cell parameters will be refined imposing the constraints for that spacegroup e. Tutorrial is used in Wilson scaling, which allows one to put the data on an approximate absolute scale. For the MAD data, there are 9 columns for each of 4 wavelengths.
CCP4 Molecular Graphics – Tutorial Contents
This should be a more reliable value than that obtained earlier, but for mosaic spread greater than 0. The contrast indicates that this is probably a correct solution, but this should now be checked! Close all other interface titorial except the main window. In the early stages of data processing, however, one has several observations of each reflection i. However, you need not stop at that point.
Alternatively, right-click on the job in the job list, go to the Input and output files. Normally the integration would be done as a background job it is times faster, because there is a big overhead associated with displaying the images in the GUI. It is assumed that the backstop shadow is circular. When things look OK, integrate the whole dataset images 1 to Scroll down and look at the table:.
Check the appearance of the “standard profiles” in the terminal window or by reading the file “mosflm. First, notice that there are now extra columns, including one holding FreeR flags:. By default, only the header information from the MTZ file is displayed.
Before starting the cell refinement, read in image 1 if it is not already displayedselect Predict and make sure that the spot positions are correctly predicted. OR you can process the data in blocks of, say, images, giving a different input mosaic spread for each block. Another possible search model is chain A of 1w2i. If the peak region is too big i. You should find that this is more difficult! If you want to remove the circle, select Circles and then Erase circles from the main menu.
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. This should be avoided if possible, and it may be worth increasing the maximum allowed value from Here is an example of how this will look:. It does not matter if they change slowly and by an amount per images that is less than 0. Enter this value via “Processing params” panel and repeat the prediction to see if it looks better. This is given just before the “average spot profile” in the “mosflm.
Within the image hutorial section, there is a small “blow-up” window in the top left corner approximately 20mm square. Using the search models generated by Chainsaw, we will now use Phaser to solve hypF. This will tell you how best to collect a full data set. This region of the detector is therefore called the “blind region”; because of its appearance in the image, tutorjal often also called the “bow-tie”, “apple-core” or “cusp” region.
CCP4 Tutorial – Contents
Exercises 2, 3 and 6 are from the Phaser web-site and are tytorial the most important ones although not very difficult with the modern version of Phaser. Reflection records are grouped into batches: The cell dimensions, resolution range and space group are carried in the MTZ file header, so that you do not normally need to enter them explicitly when running programs.
Using a higher value for the mosaic spread will result in tutrial boxes being overlaid, and some of the blue boxes will change to yellow.
The same hkl triplet may occur several times, with different instances being distinguished by different batch numbers.
A window will open displaying the contents of the MTZ file that you have created the MTZ file is a binary file, so you are actually just seeing the output of a viewer program.
NOTE that the true space group symmetry can only be established once data have been integrated. Intensity standard deviation estimations as a function of intensity tugorial, and you may need ccpp4 adjust SdAdd to get it close to 1.
The standardise procedure has added reflections, for which the structure factor amplitude is labelled as missing. To carry out experimental phasing, you will need two or more datasets. For these cases, the cell obtained from autoindexing may be better.
Check how the mosaic spread is changing.
Is this the case for this data?