10. XPS (Crystal Plate Scanner)
- 10.1 Introduction
- 10.2 XPS Menu
- 10.3 XPS Translations
- 10.4 XPS Plate ID
- 10.5 XPS Status
- 10.6 Crystallization Plate
- 10.7 Data Collection
The "XPS"-page can be accessed by selecting the corresponding tab in the main window. The page is available only if the configuration file carries the line XPS USE (see chapter Configuration File in section Input). Here, you can access all functions of the optional sample changer.
The "XPS"-page features several work areas:
- a popup window for entering physical crystallization plate parameters (see 10.1.2)
- an entry "XPS" in the menu of the main page(see 10.2)
- an area for driving x,y-translations(see 10.3)
- an area for providing an optional plate ID(see 10.4)
- an area containing the status information of a selected drop(see 10.5)
- an area containing a visual representation of the crystallization plate(see 10.6)
The crystal plate scanner (XPS) is an extension of the desktop beamline. The extension allows for mounting a standard crystallization plate, e.g. the Greiner CrystalQuick-X plates with dimensions of 85.5 x 127.8 mm and 2 drops per well. The XPS system features an orthogonal arrangement of x,y-translations for the entire plate. The motors are called XPS_X and XPS_Y from here on. To mount the XPS system, some optional components of the mardtb have to be dismounted, in particular the beamstop, the bracket holding the cooling head of a cryo-device and the tube for the cryogenic exhaust. Due to space limitations it is also desirable to dismount the entire PHI-axis. With a mounted PHI-axis, only 2/3 of the drop positions of the crystallization plate can be accessed. To access the remaining ones, the plate has to be rotated manually by 180. degrees. Since technical details are not subject of this manual, here we concentrate on the software interface and assume that the crystal plate scanner has been taken in operation with all the technical requirements. For simplicity, we assume that the PHI-axis is not present and that all positions of the crystallization plate can be accessed by driving the motors without running into collisions.
For correctly handling the crystallization plates, it is mandatory to define the physical properties of the given plate. It is likely, that only very few types of crystallization plates are being used in a lab, so the procedure of having to find suitable parameters needs to be done only very few times. Furthermore, a couple of predefined parameter sets are already implemented and new ones can easily be added any time later to a simple human readable data base file.
As a typical example here we pick the Greiner CrystalQuick-X 2-Drops plates. They have a width of 85.48 mm and a length of 127.76 mm. They come with 96 wells arranged in 8 columns A-H and 12 rows (1-12). Each well features areas for 2 drops (a-c) that are separated by a specific space. In order to let the mardtb drive from one drop to another, it is necessary to know the hor. and ver. translation from one well (e.g. A1) to the next neighbour (e.g. B1). This parameter is denominated SEPARATION and would be 9.0 mm in this example. But: since we have 2 drops per well we also need to know the spacings between drops a and b within this well. In a configuration file (see section input), the relevant parameters are demoninated DX1 / DY1 for the translation from drop a to drop b. In this example, the separaration is just a vertical translation of 3.0 mm on no horizontal movement. As a last parameter, the actual motor position XPS_X and XPS_Y for drop A-1-a should be given as reference to access all other drop positions from here on. Please note, that the origin of the coordinate system as depicted in Figure 1 is in the upper RIGHT corner if the plate is mounted in such a way that row A is sitting in the left hand corner when looking in direction of the beam (or right hand corner when seen from the perspective of the X-ray detector). This orientation is denominated as "Top". Note, that when the plate is rotated by 180 degrees within its holder, the drop in the upper right corner becomes H-12-c and the orientation is called "Bottom". The measured position here is given as ORIGIN in x and y and refers to A-1-a.
The "Crystallization Plate Setup" is a popup window that pops up when the menu item "Setup" is chosen from the XPS menu in the menu bar of the main page or when the "Setup" button is pressed in the top left corner of the graphical representation of the crystallization plate area.
The "XPS"-menu pops up if the "XPS"-button in the menu bar is pressed or if "Alt+x" is pressed while the pointer is in the main window. This menu allows for accessing different options that have to do with the sample changer. The choices are:
|Load plate data||Loads premeasured data from a crystallization plate, as produced by menu item "Save plate data"|
|Save plate data||Saves measured positions for all drops of the current crystallization plate. When saving the data, you will be asked for a file name.|
|Clear all plate data||Clears all currently stored drop positions. Good idea to do this when mounting a new plate.|
|Open Plate Setup||Opens the Crystallization Plate Setup window (see above).|
The Crystal Plate Scanner features 2 motors for x- and y-translations: XPS_X and XPS_Y. Both can be initialized at the "near end" of its translation stage by using the "Init" buttons in this area. Please note, that when seen from the X-ray source a positive translation of XPS_X tranlates the plate towards the left hand side with respect to the collimator. A positive translation of XPS_Y translates the plate upwards. When pushing the "Move" button, the selected motor is driving to the given position.
You may enter a specific identifier for your crystallization plate here. When pushing the "Save" button, the motor positions for all measured drops is being saved to file "Identifier.dat" in directory MARLOGDIR/xps. The ID string should not contain spaces and it also best to avoid special characters. Instead of using the "Custom" choice, the choices "Date", "Increment" and "Random" are available. For "Date", "Increment" and "Random", the input field on the right hand side of that menu is ignored. As ID string, either the current date and time ("Date") is used or a random string consisting of 3 alphanumeric characters ("Random") or a incremental number ("Increment").
When clicking into a specific drop in the "Crystallization plate" area on the right hand side of the XPS page, relevant information for the selected drop is displayed separately in this area. Each drop may have a defined status: either "unknown", "cleared", "assigned", "queued" or "done" (see below). For drops that have been assigned, typically a photo is available (if a video grabber card is available on the PC) and that photo will be shown underneath the status area.
This area show the current setup of the crystallization plate as seen from the perspective of a mounted detector. Please note, that the visualization of the crystallization plate may not be identical to your actual crystallization plate. For simplicity, drops a to c are either shown in a strictly vertical arrangement (as shown above) or in a horizontal arrangement, but not in mixed arrangements like can be found for instance in Swissci 3-drop plates. Still, since the relevant parameters for moving from drop a to drop b and from drop b and drop c are part of the plate definitions, you can assume that when moving from drop a to drop c you may get close to where the expected crystal sits.
For further understanding, it is important that you understand that for all
drops in a given plate, a couple of specific states are defined and
marked by a color code:
- Unknown: No specific information available (grey)
- Cleared: Existing x,y-positions have been deleted (grey)
- Assigned: x,y-positions are available (red)
- Queued: Drop has been queued for data collection (orange)
- Done: Drop has been used for data collection (green)
In the top area you will find some push
buttons with the following functions:
- Setup: Pops up the "Crystallization Setup" window when pushed. Here you have to define the physical properties of your type of crystallization plate.
- Flip: Every crystallization can be mounted in the XPS holder either with row 1 at the top or row 1 at the bottom. When pushing "Flip" the orientation is toggled. Please note, that when flipping the orientation, the previously determined x,y-coordinates for all drops become invalid, since the crystallization plate mounting is done manually and has some allowance for movements in either direction so remounting a plate always gives slightly different positions.
The next series of buttons is mutually exclusive. Only 1 choice can be active
at a time. They can be used to select drops and to perform specific operations.
- Mouse: When selected, the mouse buttons have different functions:
- Left: Single click: Show. Double click: Clear
- Middle: Assign
- Right: Move
- Show: Show status of selected drop
- Move: Move x,y to selected drop. If the coordinates have already been assigned, the stored values will be used. Otherwise, the target position is derived from geometrical parameters of the crystallization plate.
- Assign: The current x,y-positions are "good", i.e. they can be used for a data collection. Assigned values are stored in a file. An assigned drop is marked in red color. If a frame grabber is available on your PC, the software shoots a photo of the sample and stores it in directory MARLOGDIR/xps.
- Clear: Assigned motor positions for the selected drop are deleted.
- Queue: Queueing refers to a sequence of drops that can be collected automatically during a data collection. Before being able to queue a drop, its target motor position must have been assigned. When an assigned drop is selected for queueing, its color changes to orange. When a queued drop is selected again, it is being taken off from the queue and the color changes back to red. The value after the pound sign (#) indicates the position in the queue. The queue order is strictly sequential meaning that they receive their queue position from the order in which they are selected. If a queued drop at position #3 from 10 already queued positions is deselected, the remaining drops at position #4 to #10 are being moved one up. Currently, it is not implemented to insert a drop at a specific position in a queue. If you need a specific order, you will have to clear the queue and start over select drops exactly in the order you want them to be collected.
When a new plate is mounted, all prviously collected drop data become useless. Since the XPS system does not know that a plate mounting has taken place, you have to manually tell the software that you want to start with a fresh plate by clearing all drops. This is most easily done by choosing the "Clear all drops" menu item in the XPS menu of the main window. Please note, that with this procedure really all existing x,y-positions for the drops and also all existing photos of assigned drops will be deleted, unless you save them first in some other place.
When valid photos of assigned positions are available, they will be shown in the status area (see above) when selecting the drop (in mode "Show").
When collecting data with the crystal plate scanner mounted in place, moving the PHI axis is no longer possible. A data collection therefore typically consists of single exposures without further possibilities of movement. It is possible to start the data collection at the current position or to let the instrument drive to a given drop whose coordinates in x,y (i.e. positions for motors XPS_X and XPS_Y) have been established previously. Therefore, the "Exposure Settings" section of the "Edit"-page provides only input fields for exposure time, number of images to be collected and for the drop to measure which may be left empty, meaning that the XPS_X and XPS_Y will stay where they are.
If you enter a specific drop name, you have to stick to the nomenclature XYz where X is the column label (i.e. A-H), Y is the column label (i.e. 1-12) and z is the drop label (i.e. a-g). The corresponding drop must be in state "ASSIGNED", otherwise an error will be generated.
If you choose "Queue" in the option menu above, the data collection will automatically make single shots of all queued drops in the order as explained above.