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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These statistics tutorkal essential for assessing the quality of the data, whether there is anisotropy, and whether there is twinning. The output file should be automatically set to:.

Run as above, with the following differences:. Example of this window:. Click on Continue adapted Titorial menuuntil you get back to the starting menu or else click the “Timeout mode” toggle in the Processing params panel. Using a higher value for the mosaic spread will result in more boxes being overlaid, and some of the blue boxes will change to yellow.

At the top, on the line Load Parameters from command filebrowse for. Is this the case for this tutoorial

RMSBG indicates the “noisiness” of the profile it is the variation in the background after scaling the peak to We will solve the hypF structure by molecular replacement, using several programs and approaches. This procedure will output a file of structure factor amplitudes and intensities for the reflections that were collected. If not, check the values for the following parameters in the Processing Parameters window and reset them if necessary:.

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CCP4 Tutorial – Session 2

Each column has an associated type. If you want to remove the circle, select Circles and then Erase circles from the main menu. Revising point group assignment Twinning interfering with pseudosymmetry as well as low data quality make it possible to “solve” this structure in an incorrect orthorhombic space group. Look for the following:. Each line corresponds to a column of data in the MTZ file, and for each line various statistics are given.

To check how well it has worked, look at the Rms positional error between observed and predicted spot positions in the summary. Note the value for mosaic spread in the text window giving the refinement. The target has 91 residues and a Matthews calculation strongly suggests only one molecule in the asymmetric unit. The batch header contains information on how the corresponding image was recorded, and this information is used by certain programs such as SCALA.

Beware of using more than 3 segments; the calculation can take a very cp4 time and you gain very little! Exercises 2, 3 and 6 are from the Phaser web-site and are probably the most important ones although not very difficult with the modern version of Phaser.

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. Example 5 contains step by step instructions on how to use the Turorial pipeline in the default mode for experimental phasing. See also the accompanying document giving background information.

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CCP4 Tutorial: Molecular Replacement

The refined detector distance may also differ for images in different segments at the start of refinement compensating for errors in cell parameters. In fact, we able to improve on this solution. If the overlap is serious, the detector should be moved back or the collimation improved.

This opens up the loggraph viewer. Finally you are given the option of selecting the solution default yes. 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.

We will do the scaling in titorial H3, look at the output, look at excluding ‘rogue’ images from scaling, check statistics tabulated by program TRUNCATE and investigate the true spacegroup H3 or H32? Refer to these notes, and also make use of the on-line Mosflm user guide and other documents available on the same site. Thus you will have several files, obtained from different crystals, different wavelengths or ccp4 heavy atom derivatives.

After the job has finished, compare the plot for H32 with that of H3. Look at the final sd in spot positions.