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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It is convenient to combine all these files into one MTZ file.

When using ccp4i for the first time, you need to set up a project to work in. These plots confirm there is no problem tutorual twinning. Check that this value is reasonable i. Here is a collection of tutorials starting from diffraction images. Much of the information is the same as for the previous example, but there is some extra information specific to unmerged MTZ files.

CCP4 Molecular Graphics – Tutorial Contents

Project directories contain all necessary data for corresponding exercises. Please note that you can alter the layout of the loggraph window by using the Appearance, Edit and Utilities facilities provided e. However, if you do not have the output file, then it will also be available in directory DATA.

Using the search models generated by Chainsaw, we will now use Phaser to solve hypF. Leave the next line as:. Basic phasing tutorials Download tutorials and data from here: Type the input into the control window which comes up when you click on Strategy from the Main menu. The procedures that led to both false and true solutions are demonstrated including symmetry assignment and data merging.

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See the accompanying document for an example where twinning occurs. The simplest way to do this is through CCP4i. 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.

To check how well it has worked, look at the Rms positional error between observed and predicted spot positions in the summary. Using a new ligand description Description: Try reading in another image, run Find spots and Autoindex again. Giving the keyword NULLPIX will mean that any predicted reflection that has a pixel within its measurement box with a value less than will be rejected during integration.

This should get smaller if more than one cycle of refinement has been performed. The Loggraph viewer will now be displayed as before. Integrate the 10 images again, and compare the resulting profiles with those obtained using the default value. 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 crashes should never happen of course!

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:.

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CCP4 Tutorials

If some data have already been collected: The graphs in Acentric Moments of You need to repeat steps to or for all these. We will do the scaling in spacegroup H3, look at the output, look at excluding ‘rogue’ images from tutorisl, check statistics tabulated by program TRUNCATE and investigate the true spacegroup H3 or H32?

Scroll down and look at the table:. This will tell you the maximum angle at 5 degree intervals.

CCP4 Tutorial: Session 1 – Introduction

Cell and symmetry information is obtained from the input file and doesn’t need to be entered. Tutorisl resolution of the circles is given in the Output panel. When the job has finished, return to the Scala – Scale Experimental Intensities window, select the newly reindexed MTZ file as input for scaling and change the job title.

Programs use these names to identify the columns that are to be used. Try varying the mosaic spread Processing params panel and see the effect on the predicted pattern select Predict from the main menu after any change in mosaic spread.