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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Integrate the 10 images again, and cc4 the resulting profiles with those obtained using the default value. NOTE that the true space group symmetry can only be established once data have been integrated.
CCP4 Workshop: Lecture Notes and Tutorial Material
If they are changing more than this then there could be a problem with processing the data there is not much you can do about this. Remember that, by default, although the mosaic spread is refined, the program tytorial uses the INPUT value. The use of these names and the CCP4 harvesting routines is very strongly recommended.
At the end of the tutorial, there are suggestions for web-based options. Therefore, go straight to the one which is the most interesting for you. The program will then come up with 2 segments of 15 degrees to get the most complete data possible.
Refinement with ligands and covalent links Download and unpack tutorial data jligand. Close or Quit all other interface windows except the main window. On the cccp4 line, turn off Create full unique set of reflections using the radiobutton. In this exercise, we examine an unmerged MTZ file. There are many ways of approaching this, and the different tools will give slightly different assessments. This should fill in the bulk of the interface window. Check against the contents of the PDB file why they should have such a value.
The second is more involved and investigates the balance between completeness tuyorial non-isomorphism when merging multiple lysozyme datasets. Finally you are given the option of selecting the solution default yes. We also need to enter an estimate of the number of residues in the asymmetric unit. Alternatively, right-click on the job in the job list, go to the Input and output files. The following tutorial deliberately does not make use of the web, so that it can be run anywhere.
The same hkl triplet may occur several times, with different instances being distinguished by different batch numbers. In fact, we able to improve on this solution.
You can test the effect of smaller rotations than 30 degrees by:. The direct beam coordinates can be input in the Processing params panel Beam X and Y.
Each has two chains in the asymmetric unit, either of which could be used as the basis of a search model. Such pixels are excluded from the integration. 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.
In the case, the default format statement is slightly wrong, and needs to be changed to:.
CCP4 Tutorial: Contents
Click on Circles in the Main menu to display resolution circles. If you want to remove the circle, select Circles and then Erase circles from the main menu. The so called “cumulative intensity statistics” tabulated by TRUNCATE and plotted by LOGGRAPH provides the only point at which you will be able to detect tuorial twinning when the two lattices of ccp twin components exactly overlap, and every measured intensity is actually the tugorial of two intensities.
Note that you may get better tutoriql using a smaller oscillation angle than that suggested here. If you need another image preferably at a very different phi value to get the autoindexing to work, click on Read image to get the new one, and then on Find spotsand then Autoindexing.
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.
To check how well it has worked, look at the Rms positional error between observed and predicted spot positions in the summary. Use the cursor and the cross-hairs to determine which residues they are. Search models can also be prepared using Chainsaw. Select the Data reduction module, and open tutrial Integrate Images task window.
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. There is native data in H32 to 1. Sometimes you can change processing parameters in response to these warnings, using the keywords given in the warning but not always!!
See also the accompanying document giving background information. Here is an example of how this will look:. The input file runit contains the minimum information required to start analysing the data:.
The program will pause for detector parameter refinement for the centre of the image.
CCP4 Tutorial – Molecular Replacement
See how sensitive the autoindexing is to the main beam values. The file contains 6 columns; 3 holding the hkl indices, and 3 containing data. Check the variation in B-factor with image B v rangeand if there is no real variation less than 2 or 3 units, either positive or negative it is best to turn off the B-factor refinement.
If this is not the case, then change the rejection criterion to avoid rejecting these reflections e. You can exclude a given batch from the scaling.
If the mosaic spread is very high 1 degree or more a significant number of reflections will ccp flagged as “too wide in phi” green boxes. The refined detector distance may also differ for images in different segments at the start of refinement compensating for errors in cell parameters.
To carry out experimental phasing, you will need two or more datasets.
This program converts intensities to amplitudes, and also compiles some useful statistics.