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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CCP4 Tutorial: Molecular Replacement
The rows correspond to different reflections, and the columns correspond to the 6 columns of data described in the header. Refinement with ligands and covalent links Download and unpack tutorial data jligand. Look for the following:. You should find that this is more difficult! Now look at the table of statistics near the bottom of the display window:.
Here vcp4 a collection of tutorials starting from diffraction images.
This table also shows shell and cumulative R-factors. The simplest way to do this is through CCP4i.
In this case H3 high completeness can be achieved with a 40 degree rotation in two 20 degree segments:. This should be a more reliable value than that obtained earlier, but for mosaic spread greater than 0.
Example 8 illustrates a frequent problem with the space group assignment in the presence of pseudo-symmetry and twinning and how an incorrect assignment may affect MR structure solution. If you want to remove the circle, select Circles and then Erase circles from the main menu.
In the case, the default format statement is slightly wrong, and needs to be changed to:. Each has two chains in the asymmetric unit, either of which could be used as the basis of a search model.
The program will then come up with 2 segments of 15 degrees to get the most complete data possible. The maximum reflection width can be changed as follows: This is the best indicator of data quality.
The program will pause for detector parameter refinement for the centre of the image. Check that this value is reasonable i. In the Crystal Parameters folder, verify Space group H3 the true space group symmetry can only be established once data have been integrated.
When using ccp4i for the first time, you need to set up a project to work in.
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. This example will take the output from step 2a.
This ratio is tabulated in Standard deviation v. It is also likely that the number cxp4 overlapped reflections will increase, as will the number of reflections with green prediction boxes.
Some entries are given as “? You can test what completeness you would get from starting somewhere, as long as the range is within the range recommended above by the program. The Zoom feature has been disabled on some SGIs because it can cause the terminal to freeze.
CCP4 Tutorial – Session 2
You have already completed the native set, and the MAD measurements extend to a lower resolution. On subsequent images, it will only pause once per image.
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 graph of the 2nd moment is the clearest. The information that is displayed comes from the header of the MTZ file.
These will be dealt with below, so click Dismiss. Close all other interface windows except the main window. Tutoriwl it is above 0. Output from the programs or text from tutoiral interface is given in green.
By default, only the header information from the MTZ file is displayed. RMSBG indicates the “noisiness” of the profile it is the variation in the background after scaling the peak to Click on List More Info at the bottom of the display window. Errors in the initial cell may give different values, especially if more than one segment is being used.
A dialogue box will appear. It is considered good uttorial to add in all other reflections appropriate to the spacegroup and resolution, even if there is no data for them “completing the dataset” and to add a column of free-R flags at this stage to the master dataset. Such pixels are excluded from the integration. This model should be submitted to 20 cycles of automated refinement, then checked manually against 2mFo-DFc and mFo-DFc maps, using a graphics program such as Coot.
Therefore, go ccp to the one which is the most interesting for you. Predict the reflections, then use Find hkl to locate the offending reflection in the image you must give the measured indices, the first set of values in the ROGUES file, when doing this.
If you have done more than one integration run during your MOSFLM session, you will find multiple entries of the tables. In the following instructions, when you need to type something, or click on something, it will be shown in red.