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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In some cases the tutorials also go on to phasing and structure solution. Integrate the 10 ccl4 again, and compare the resulting profiles with those obtained using the default value. If the program finds any “Bad spots” rejected reflections it will ask the user if they wish to reclassify the spot or inspect it. Check against the contents of the PDB file why they should have such a value.
When the mouse is in the image display, clicking middle mouse button will improve the resolution of this window, but it can no longer be moved. 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.
Close all other windows except the main window. Adjusting the resolution limits also helps.
The same hkl triplet may occur several times, with different instances being distinguished by different batch numbers. HypF-ACP sulphate and phosphate complexes deposited as 1gxt and 1gxu respectively. This procedure will output a file of structure factor amplitudes and intensities for the reflections that were collected. This type of file has only one record for each set of hkl indices, and is the type of file one has after merging together all different observations of a particular reflection.
CCP4 Tutorial: Session 1 – Introduction
If you do exit, follow the instructions at the end of this section on how to restart from saved parameters. Experience has shown, that most people benefit from being familiar with the program before learning about the STRATEGY option, which therefore in this tutorial features only after integration.
It is often necessary to integrate the images several times before the refinement converges; if the shift in cell parameters is more than 2. It does not matter if they change slowly and by an amount per images that is less than 0. Make a note of these values, then mask out the backstop shadow by clicking on Keyword input and typing in backstop centre X Y radius Z X, Y and Z are in mm and then run to get back to screen control. Sometimes you can change processing parameters in response to these warnings, using the keywords given in the warning but not always!!
The program will then integrate these images in turn. There should be 7 peaks above the threshold, many of which are true symmetry equivalents.
CCP4 Tutorial: Session 2 – Data Processing and Reduction
In this case H3 high completeness can be achieved with a 40 degree rotation in two 20 degree segments:. The previous example looked at a so-called merged MTZ file. This will not cause a problem as long as there are a reasonable number of background pixels that are not overlapped ideally more than Click on List More Info at the bottom of the display window. Exercises 2, 3 and 6 are from tuhorial Phaser web-site and are probably the most important ones although not very difficult with the modern version of Phaser.
CCP4 Tutorial – Contents
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. Note however that the positional residual will be higher for weak data, as the spot positions are not as well defined. Each column has an associated type. If tutoriaal data cccp4 already been collected: Click on Clear spots and hit Enter to remove the crosses from the image.
See how much the cell parameters change.
You can test what completeness you would ccp44 from starting somewhere, as long as the range is within the range recommended above by the program. You have processed this data. This ratio is tabulated in Standard deviation v. Hit Enter to the first query, then give the first and last image numbers: The cell parameters derived from the autoindexing will now be refined using the observed spot positions note that the a and b cell parameters are not equal in the initial cell.
It is recommended to set up a new ccp4i project for each of the examples cp4 set the project directory as indicated below. 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.
Rejecting a significant number of the tutirial reflections can give problems in structure solution. 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 fcp4 should never happen of course! Read in the image using Read image in the main menu.
CCP4 Molecular Graphics – Tutorial Contents
This will open a Task window. 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. Some of the residues have Bfactors of 0.
If you want to try another solution from the list, reply N and you will be prompted to select a new solution. The cell parameters will be refined imposing the constraints for that spacegroup e.
There will probably be some diffraction spots which are not covered by a prediction box; this means that with the current mosaic spread, these spots would not be predicted.