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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To test the higher symmetry, do the following:. See if there is anything odd about the spot.

CCP4 Tutorial: Session 2 – Data Processing and Reduction

For orthorhombic or lower symmetries, the use of two or more images will give better estimates of the cell parameters, and this is recommended. 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.

Enter this value via “Processing params” panel and repeat the prediction thtorial see if it looks better. Such pixels are excluded from the integration. Then do for example:. If you want to try another solution from the list, reply N and you will be prompted to select a new solution. If the program finds any “Bad spots” rejected reflections it will ask the user if they wish to reclassify the spot or inspect it.

Target is the acylphosphatase-like domain of hydrogenase maturation factor HypF from E. Note that when you run the autoindexing the second time, by default it will use the symmetry you chose H3 when you first ran the autoindexing. If it is more than two pixels, the autoindexing may have failed if you do not know the pixel size, look in the “mosflm. The ROGUES file gives you the image Batch on which the reflections have been recorded for partials, this is the image nearest the centre of the tutoriql, so you may need to look on the preceeding and following image as well.

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Run as above, with the following tuotrial. Check the Number rejected v range graph for oddities – this may tell you something about ‘rogue’ images.

CCP4 Workshop: Lecture Notes and Tutorial Material

It may be useful to check the residual for the central region of the detector in these cases. If the overlap is serious, the detector should be moved back or the collimation improved.

It is generally possible to collect high completeness data without doing yutorial full rotation range. Thus fcp4 will have several files, obtained from different crystals, different wavelengths or for heavy atom derivatives.

Alternatively, right-click on the job in the job list, go to the Input and output files.

CCP4 Tutorials

See also the accompanying document giving background information. Crank pipeline for experimental phasing Automated structure solution using Crank pipeline and inflection point data. Some of the residues have Bfactors of 0. If it is not because the crystal has moved then get a new orientation matrix for each segment, using ONLY spots from that image Select images. This is the best indicator of data quality.

Note that you may get better data using a smaller oscillation angle than that suggested here. You have now prepared three search models based on 1v3z, and used Molrep and Phaser to do the molecular replacement. Select the Data reduction module, and open the Integrate Images task window. The target has 91 residues and a Matthews calculation tutoroal suggests only one molecule in the asymmetric unit. The current Import job should be at the top. Adding glycan to ccp4 protein crystal structure and refinement of the completed structure Project directory: Using the search models generated by Chainsaw, we will now use Phaser to solve hypF.

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If it were much further away, autoindexing would not work. Find out the centre and extent of the backstop shadow using the left mouse button and looking at XC and YC in the Output panel. In fact, we able to improve on this solution.

It uses two different ways of estimating the standard deviations of the observed merged intensities:. For these data, the true direct beam position is within 0. You need to repeat steps to or for all these. There are many ways of approaching this, and the different tools will give slightly different assessments. Blind region reflections have green prediction boxes. Click on the headings to expand or collapse each section. The program will now integrate these images, and use the resulting intensities to refine the cell parameters, crystal orientation and mosaic spread using the post-refinement procedure.

The best way to locate the direct beam position is to look at a powder diffraction ring e. This tuutorial on the mosaic spread and minimum separation. If not, revert to the original value.

Leave the next line as:. In the main display window, the batch header for each batch is displayed. Various processing parameters can be entered in the tutoeial params” panel on the left.

The following tutorial deliberately does not make use of the web, so that tutoria, can be run anywhere. Check against the contents of the PDB file why they should have such a value.

Other MR examples can be found at the end of this tutorial, and at: This should get smaller if more than one cycle of refinement has been performed.