Previous: Starting the HKL GUI: an Overview, Next: Spot size and spot shape
Now we can start to do peak search and index on the first set. Click the "Display" button in the middle bar:
The display window with the first image of the first set will pop up. Make sure the arrow in the "Frame" button is pointing upwards. If it isn?t, right click the frame button. Then do a peak search by pressing "Peak Sear" in the display window, followed by a series (normally ten) of middle clicks on the "Frame" button. If you have a two-button mouse, simultaneously click the left and right mouse button, to reach the same goal. While you?re doing this, you will see the found peaks in red in the image display and the filename numbers up in the top left hand corner of the image. After, say, ten images click OK. This will finish the peak search. A file "peaks.file" has now been created in the working directory.
If we now press the tab of the next level: "Summary", you can have a look at the sets and files we are looking at and their properties. Depending on which tick boxes have been activated, you can see what the properties are of each set:
Now we have done the peak search, we can go to the next level: Index/Refinement/Integration. This is another big window, which can be split into sub-sections: "Sets pending", "Resolution", "Refinement options", "Integration Box", "Refinement information" and controls.
First go to the "Controls" part and click "Index"
The GUI will show the word "Indexing" and will pop up a window with the results of indexing:
Select the solution that you like most and click OK. If you have changed to another Bravais lattice, the program will do a transformation and come up with the solution in the new Bravais lattice. Only if you click "Close" the window will disappear. It can be popped up again by clicking the Bravais Lattice button.
To refine the solution you can select the parameters to be refine in the Refinement options area. There you can also see buttons for Fit all, Fix all or Fit Basic. Normally you would start to refine the basic parameters by clicking Fit Basic, followed by Refine. The program will then refine the number of cycles as indicated. The results of refinement are shown in the Refinement Information area and are updated after every cycle of refinement. In the display area you will see the predicted reflections (hopefully) on top of the observed predictions. The "full" reflections are displayed in green, whereas the "partial" reflections that have not fully passed the Ewald sphere will be displayed in yellow.
The refinement information displays the progress of the refinement.
The three columns are the actual refined value, the shift and the error. Refinement has converged if the shifts are (close to) zero.
The center of the detector is displayed as a cross (+). The actual primary beam position is displayed with a square. At theta=0, the two will more or less superimpose, with theta offsets, the two will be in different places.
The resolution area now shows three choices for the high-resolution limit: Edge, Half Corner and Corner. The effect can be seen at the resolution limits that are calculated by the program after a refinement run. Next to these three choices, you can always fill in the resolution limits by hand.
Circles of equal resolution can be drawn in the image by filling in the resolution "bins" and pressing the button "Resolution circles". You can remove all circles by typing "0" in all five fields.
The resulting image will look like this:
Looking at "Crystal information" one can see the final parameters of refinement. This will pop up a window with all relevant info on the crystal. In here one can change the space group, the reference zone of the orientation and give some more info on the crystal.
The Reference Zone is also mentioned in the "Controls" area. In Denzo the orientation is described as a basic orientation with three additional rotations. For e.g. P212121 there are eight different rotations to get to the same orientation. In the present version it is now possible to change the way the orientation is described. This may be useful for protein applications, where one knows exactly how the crystal is mounted with respect to the goniometer (e.g. a parallel to the beam, b along the rotation axis and c perpendicular to the other two), but for chemical crystallography this is not really relevant.
After setting the spot size and shape and the mosaicity as described in the following two sections of the manual, you should check the other set if all the parameters are OK, by clicking set 2 in the "sets Pending" window. For a theta offset you should turn off the elongation spot and the resolution should be higher. Normally all other parameters can stay the same.
