Harvesting Crystals

Once you find an experiment hit, you can virtually harvest your crystals and assign them to a Synchrotron Trip.

To harvest crystals:

Open an experiment with crystals.
Then, go to the Drop(s) tab in the Images tab set.
Double-click on a well that contains the crystal you want to harvest in Canvas view, to open that well in Drop view.
Click the Harvest Crystal button and draw a rectangle around the crystal location within the drop.
Once you have drawn a box around the crystal, the Crystal Definition window will appear. Here, you will need to define the following:

Note: You can see the drop from the Image Preview on the right side of the Crystal Definition panel.

Crystal ID. This field is automatically populated by ROCK MAKER.

Crystal Name. Type a name for your crystal in the Crystal Name box, if you do not want to use the default name provided.

Note: You can change the format of the default crystal name in ROCK MAKER Global Preferences. For more information, read System Properties.

Owner. Select the owner of the harvested crystal from the user list.

Project. Shows which project you harvested the crystal from.

Experiment. Shows which experiment you harvested the crystal from.

Plate. Shows which plate you harvested the crystal from.

Protein. Shows the name of the protein/sample that the crystal is made of.

Sample. Shows the well ingredients found in the source well for the crystal.

Synchrotron Trip. Select the Synchrotron Trip from the dropdown list.

Date Frozen. Select when the crystal was frozen.

Dewar. Select the Dewar where the crystal is located from the dropdown list.

Puck. Select the Puck where the crystal is located from the dropdown list.

Position. Type the pin number where the crystal is stored in within the puck.

Data Collected. Select the checkbox if diffraction data has been collected on the crystal.

Note: Data Collected can only be selected if the Data Collection Date is in the past.

Structure. Select this checkbox after you have resolved the structure of your protein from the data collected.

Note: Structure can only be selected if the Data Collection Date is in the past.

Resolution. Type the resolution at which the structure was finally refined.

In the Cryoprotectant panel, define the cryoprotectant you used prior to freezing your crystal:

Note: You are required to fill in the cryoprotectant information.

Click the Load Saved Cryoprotectant button to choose from existing cryoprotectants that have been used before.

Click the Load from Sample button to use the crystal’s source well ingredients as the cryoprotectant. Select Yes when the dialog window appears to confirm your selection.

Click the + button to manually add the cryoprotectant by defining these fields:

Ingredient. Required field. Type the name of the ingredient that you are going to use.

Conc. Required field. Type the concentration of the ingredient that you are going to use.

Conc. Unit. Required field. Select the concentration unit of the ingredient that you are going to use.

pH. Required field. Type the pH of the ingredient that you are going to use.

Protocol. Enter any relevant details about how the crystal was frozen.

Note: If you want to save your current cryoprotectant selections for future use, type a descriptive name for your cryoprotectants in the Save Cryoprotectant as box. Your selections will be saved when you click Apply after you are finished inputting your data in the Crystal Definition window.

In the Soaking panel, you will define the name of any compound (or ligand) that you soaked your crystal in, as follows:

Click the + button to add a new soaking compound, and then define the following fields:

Name. Type the name of the compound used.

Conc. Type the concentration of the compound.

Conc. Unit. Select the concentration unit of the compound.

Time. Type the duration of time for which the crystals were soaked.

Text Info. Add any additional information relevant to the soaking process.

Browse a document from a directory and attach it in the Attachment box of this crystal record, if desired.
Type any additional information regarding the crystal in the Notes field, if desired.
When you are finished defining your crystal, click Apply to mark the crystal as harvested. A harvested crystal icon will appear on the experiment plate icon.

Note: Harvested crystals that do not have their synchrotron trip, puck, and dewar defined can be found by opening the project the crystal came from. Crystals with their synchrotron trip, puck, and dewar already defined can be found in the relevant Synchrotron Trip in the Crystal Tracking node on the Explorer.

Harvesting Crystals

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