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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Check that this value is reasonable i.

In the following instructions, when you need to type something, or click on something, it will be shown in red. This model should be submitted to 20 cycles of automated refinement, then checked manually ccp44 2mFo-DFc and mFo-DFc maps, using a graphics program such as Coot. Close all other windows except the main window. A dialogue box will appear. It is not unusual for this to be higher for two images than for a single image, because the crystal orientation may have changed between collecting the two images.

Note however that the positional residual will be higher for weak data, as the spot tutrial are not as well defined.

CCP4 Tutorial: Session 2 – Data Processing and Reduction

It uses two different ways of estimating the standard deviations of the observed merged intensities:. For these cases, the cell obtained from autoindexing may be better.

The program first asks if you want to change the cutoff for tutogial individual reflections from the refinement:. It is also likely that the number of overlapped reflections will increase, as will the number of reflections with green prediction boxes.

CCP4 Tutorial – Molecular Replacement

In the new window give a new title such as. Irregular backstops can be dealt with using the NULLPIX keyword, providing all pixels in the shadow have pixel values less than tutorizl “active” part of the detector. This protein has a Hg derivative.

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These names will be used to identify the data for Data Harvesting and to categorise the data within MTZ data structures. In the MTZ format, the column names are not fixed, and neither is the order of the columns. Various processing parameters can be entered in the “Processing params” panel on the left. At this stage, we can have a look at the anomalous Patterson for these data. 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.

Giving the keyword NULLPIX will mean that any predicted reflection that has tuutorial pixel within its measurement box with a value less than will be rejected during integration.

It will display a new window showing the average spot shape for the centre of the image, and the positional residuals. Search models can also be prepared using Chainsaw. You can test the effect of smaller rotations than 30 degrees by:.

Another source of information is “on-line” help. By default all found spots from all images will be used in autoindexing, but any combination of images can be selected using Select images.

The program will now cxp4 these images, and use the resulting intensities to refine the cell parameters, crystal orientation and tugorial spread using the post-refinement procedure. You need to repeat steps to or for all these. The final column CORRLN is the correlation coefficient between that profile and the one for the centre of the detector.

For answers to problems not resolved by these sources, feel free to e-mail Harry Powell. In fact, we able to improve on this solution. Remember that, by default, although the mosaic spread is refined, the program actually uses the INPUT value.

You can find the current values in the mosflm. Look for a gap cccp4 around e. It is best to be conservative and use the lower symmetry which still matches the information we have about cell parameters and systematic tutoiral and the entries for the cell parameters. 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.

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Often you will use the output file of one job as the input file for the next job.

The same hkl triplet may occur several times, with different instances being distinguished by different batch numbers. We also need to enter an tutoral of the number of residues in the asymmetric unit.

At the end of refinement, the distance should be the same for all images, typically to within 0. The procedures that led to both false and true solutions are demonstrated including symmetry assignment and data merging.

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.

See if there is anything odd about the spot. It is convenient to combine all these files tktorial one MTZ file. Click on the headings to expand or collapse each section.

Tutoria, what is in the small window because you have the option of changing both the beam position and the position and size of the backstop; you only want to do the latter!

In some cases the tutorials also go on to phasing and structure tutoril. We will see later that all but the 0,0,0 peak are symmetry equivalents. The search model has a moderately low sequence identity with the target and therefore the majority of the side chains are incorrect. Target is the acylphosphatase-like domain of hydrogenase maturation factor HypF from E.