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Getting Started

The beamline workstations are used to control the beamline and store the data and analysis files on a common file server. Log in on these computers using your user name and password. Remember that Unix is case sensitive.

We recommend creating subdirectories in the /data disk for each data set you collect; e.g.:

[bl92b]~ 1>mkdir /data/yourid/crystalname

Subdirectories are also automatically created when starting data collection from the data collection or screening tabs.

Starting Software

To start Blu-Ice, click on the Blu-Ice logo on the desktop command bar and select your beamline from the pop-up menu. If you wish to run Blu-Ice from an SGI workstation (not recommended!) use the toolchest to open a Unix shell on the local host and type go on the command line prompt.

Blu-Ice Interface

The Blu-Ice GUI is organized into tabs. Different functions of the software can be accessed by clicking on the tabs. Users are allowed to enter the Hutch, Sample, Collect , Screening, Scan , Users Tab and Log Tab.

Status Bar

The status bar at the bottom of the screen shows the status of the software and beamline hardware.

The section on the left hand side shows one of three colours depending on the condition of the beamline:

  • Green : the detector is online, the door is closed and the beamline is ready to run, as in the example shown above.
  • Yellow : something inside the hutch is moving or the door is open. The message in the window will explain what is happening. In the example below, the hutch door is open.
  • Red : there is an error condition that needs action. Generally when a user first runs Blu-ice, they will need to log on to the system using their password (in the "Users" tab). If they have not done so then the message "logged out" will appear.

The next indicator displays the SPEAR current (usually between 100 and 80 mA when the beamlines are open).

The Abort button allows the user to interrupt the current operation. All motor motion taking place at the time of the abort will be immediately interrupted before the motors have reached the final destination (except for the robot), so use this button with caution. Most Blu-Ice tabs have a "Stop"or "Pause" button which allows interrupting operations more cleanly.

The "User" button is used to become the active client with permission to initiate experiments and move motors. Only one user at a time may be active, which prevents multiple users trying to move motors at the same time. This button is set to "passive" by default; clicking the button will then show "active" in red. The button will change to passive mode by clicking on it when it is active or when some other Blu-Ice instance or Web-Ice becomes the active client.

The final indicator on the status bar tells you whether the shutter is open or closed, and will display this during normal data collection or screening. By clicking on the button itself, you can toggle between open and closed but this is of little use during normal data collection and screening.

Network status

The Blu-Ice GUI may be used by multiple users on different computers simultaneously. However, only one user at a time can control the beamline; the other instances of the GUI behave as passive observers (this is the default when starting Blu-Ice). In order to gain active control of the beamline, the network status must be Active. To become an active user, click on the word Passive written in black at the bottom of the screen next to network; the text will change to Active.

If the status reads Offline, you are not enabled to run Blu-Ice on that particular beamline; go to the User Tab and type in your password. If the GUI is still offline, contact the beamline support staff.

Message Window

The message window just above the status bar displays detailed information regarding beamline control operations. This area can be enlarged by dragging the upper edge of this window with a mouse. For specific information about the experiment, see the Log tab. Summaries of fluorescence scans are also available from the scan tab.

Log Tab

The Log tab can be used to view and save a log of the experiment. The log displays the value of the detector and beamstop to sample distance, beam size and attenuation, energy, data collection mode and (for screening) the sample cassette spreadsheet name at the start of each screening or data collection run; it also lists the full path for each file generated during the experiment and the starting phi value for each diffraction image. Error messages are also displayed. To stop the log tab contents from scrolling during inspection, check the pause radio button at the top of the tab; clicking the refresh command button will update the contents of the log.

Saving and Resetting the Log

To save the contents of the log tab to a file, click on the download command button. This will open a file browser window where you can select the directory and file name to store the log file. Trying to write the log to an existing file will result in an error, so that you cannot accidentally erase old logs). The log file is saved in ASCII format.

To start a new log file, click on the new log button. This will clear the log tab contents and start a new log. If you do this by accident, you may ask the beamline support staff to retrieve the log contents for you.

Users and Staff Tabs

  • The Users Tab lists the user names, status and location of all the Blu-Ice instances open at the beamline.

  • If your Blu-Ice session has expired, you will be requested to enter your Unix user ID and password.

  • Users can not access the Staff Tab; staff uses this for beamline conditioning.