KappaCCD User Manual   Revision 1.10, Last Update 1-July-1998

Indexing Images

Default peak search.  Click with the left-mouse button on the <Peak Search> button. Click with the middle-mouse button on the <Frame> button. The indexing will extend to the second frame. Repeat adding frames to index until you have 10 frames or at least 10 degrees of data. Press the OK button to end the peak search procedure. More control over peak search  Click <More peaks> to lower the acceptation thresshold of the peaks. Click <Size peak down> to enable acceptation of closely spaced peaks. Note that you can only see the size change in the display Zoom window. The chosen settings will remain in effect for the next images as well.

• Progress to the Denzo-SMN program index card.

Index card

The index card has default settings for check boxes the first time it is entered.
If you have no prior knowledge about your crystal, use the proposed settings.
Use the full resolution of the image data that are available initially.
Use a starting mosaicity of 0.5 degrees or a value typical for your type of crystals.
The displayed lattice type does not influence the indexing process, so you can set it to any likely value.

For box sizes and pixel sizes use a safe value in the middle of the displayed range. You should adapt the values according changes you have made during peak search concering peak size and acceptation level.
Clear the input field for longest vector or fill in a safe value when more information about the crystal is available.

When all values are correct and peak searching was performed, press the <index> button.
Indexing will bring up a cell selection window and a Refinement window with chi-squared information.

Cell lattice selection

The cell selection window displays colors for every cell according the Figure of Merit (FOM) for that cell. Green values are acceptable, black indicates doubtful and red means impossible. The absolute values of the FOM may vary with crystal quality.
In general one starts with the green entry of highest crystal symmetry by marking the check box in front of your selection and pressing OK.
If the cell selection is changed from the initial setting, the cell selection window will reappear and you have to press OK once more.

 The system will now display the first image of the indexed set and will indicate the searched peaks in that frame. No predictions are shown yet.
The menu will change over automatically to the Manual Refinement card.