Bruker SMART X2S Remote Access Information

The following information is provided primarily for those who want to use the Bruker SMART X2S from a remote location. The SMART X2S at Otterbein can be controlled remotely using the the Zethus CyberLab remote access node. The following documents provide information about setting up remote access, controlling an experiment, and downloading structure data and reports. (The information on this page is also available as a PDF download).


SMART X2S Remote Access: Initial Setup

The SMART X2S at Otterbein can be accessed remotely using a software package called CyberLab. The CyberLab software is a “Java Web Start” program, meaning that it can be started just like a locally installed program, but is actually running via the web. Detailed instructions for downloading and installing the CyberLab software are given below.

Note: The Zethus CyberLab software only runs under Windows (XP or Win7). It is not compatible with OS X.

Downloading the CyberLab software (once per computer)

Point your browser to: http://www.zethussoftware.com/tools-1.4.x/

When asked to log in, Username is otterbein, password is (contact Dean Johnston for password). Then select CyberLab UserTool. This will download a “Java Web Start” (.jnlp) file. The program will be downloaded and run from the Internet. Whether it runs automatically will depend upon your browser. You may have to go to your downloaded items folder and double-click on it.

Defining the Otterbein SMART X2S Node (once per computer):

After starting the CyberLab software for the first time, you will need to tell the software how to find the Otterbein X2S Node.

  • Click the small grey triangle to show the Cloud Definitions box
  • Right-click in the Cloud Definitions box and select Add Cloud
  • Enter the following information:
    • Otterbein-XRay in left box,
    • and 205.133.226.123:9001; in the right box (see figure below)
  • The completed definition should look like the figure below:
 

SMART X2S Remote Access: Logging In

Logging into the SMART X2S via CyberLab will allow you to remotely access data files and reports, view scheduled sessions, and view/control the SMART X2S instrument in real time. Note that you will only have permission to control the instrument during scheduled instrument sessions (viewable under the Session Schedule tab). You can access files at any time.

Each institution will be assigned an individual user identity (otterbeinUser, wittenbergUser, etc.) and password. These will be given out individually.

Name: otterbeinUser (for example)
Key: •••••••• (contact Dean Johnston for your Name and Key)

Logging in give a window similar to that shown below:



In this case, a session has been created for OtterbeinUser. Clicking on the large orange arrow will open a view/control session window. Instructions for viewing a session can be found in the Remote Viewing / Remote Control instructions. (next)



SMART X2S: Remote Viewing / Remote Control

When you log in to the CyberLab remote access system, you will only see those sessions for which you have been given permission to join. If you have scheduled a session and do not see the large orange arrow, please contact Dean Johnston. Here is the window for OtterbeinUser with an active session:



Clicking on the large orange arrow brings up a new VNC session with information about the current session. Click the small green and white X in the top right corner to hide the information screen. Shown below is a screenshot from an active data collection session:



You can use your mouse to control the instrument as the data collection is running. Simply close the window to stop the remote viewing session. See Chapter 4 of the Bruker SMART X2S User Manual (PDF) for more information about automated data collection and structure solution.


SMART X2S Remote Access: Accessing Files

Once the data collection and structure solution process is complete, the data files are burned to a CD (optional, but recommended) and archived to the data storage node. The data generated by the experiment and processing are archived into three zip files:

  • frames.zip - the raw image files or “image frames”
  • work.zip - the data processing files generated during indexing, integration, absorption correction, structure solution and structure refinement
  • report.zip - the final report, generated as an HTML page with embedded Jmol figure

In most cases, when a satisfactory solution is found, you need only to download the final report, i.e., the report.zip file. This zip file contains both the full report (report.html) and the structure information (report.jmol). The report.jmol file is a crystallographic information (CIF) file, even though it is given a “.jmol” extension.

Sample Naming Convention (note: changed starting January 2012)

The following convention will typically be used for all samples:

  • The first two letters represent the organization / institution
    • OT = Otterbein University
    • DU = Denison University
    • OW = Ohio Wesleyan University
    • WT = Wittenberg University, etc.
  • The next three digits will simply be a numerical ordering for all samples
  • Appending letters A, B, C, etc. if needed for repeat data collections on the same sample

Example - a recent sample collected at Otterbein was titled OT007. Note that the three files archived always have the same file names. But they will use the above convention for the sample name. Additional information is associated with each file, including formula, date, and even the final R-factor.

Exploring Archived Files

Log into the SMART X2S Remote Access node as described above under Logging In. Once logged in, click on the Files Explore tab.



You can browse by Formula or Sample (Name), or you can search by Date Modified/Stored. (Note: searching by Name, Origin or Owner is not very useful since those parameters are essentially the same for every experiment.)

Example #1 - Finding and Downloading Data for an “Ylid” Sample

The reference sample for the instrument is 2-dimethylsulfuranylidene-1,3-indanedione (C11H10O2S), and is commonly called the “ylid” sample. This sample gets run periodically to check instrument performance.

  • In the Files Explore window, click on the plus sign to the left of the Formula item to expand the list of formulas entered for the various compounds.
  • Double-click on the (first) entry with the formula C11H10O2S - the symbol to the left of the formula changes to a check mark.
  • Click on the Search button at the bottom of the window - a list of all files with the selected formula is generated (shown below)


The window above shows a total of three different experiments, each generating three files (frames.zip, work.zip, report.zip). We will select one experiment and download just the report.

  • Right-click on the first report.zip file and select Get selected files (see below). The file will be downloaded to the location you choose.


After expanding the report.zip file (creates a report directory), opening the report.html file in a browser shows the full structure report.



Opening up the report.jmol file in a program like Mercury to generate ORTEP representations (below), packing diagrams, etc.



Example #2 - Finding Data By Date Stored

You can also search for files by the date they were originally stored on the storage node.

  • In the Files Explore window, click on the Search tab.
  • Click the checkbox next to the Stored item.
  • Select or enter the date or date range of interest. (In this case we’ll see what data was collected on September 2, 2011)
  • Click on the Search button at the bottom of the window - a list of all files stored on September 2, 2011 is generated (shown below)


In this example, the second sample (OT110902B) did not generate a report.zip file because the experiment was aborted before the data collection and processing was completed. It is, however, still possible to download the “raw” data and fully process it using the APEX2 software suite (see the Bruker APEX2 User’s Manual for details).



SMART X2S: Summary of Generated Files

Archive File Description File Purpose File Names / Extensions
frames.zip: “raw” image frames generated during data collection
    image frames matrix _0x_yyyy.sfrm – survey frames used to evaluate crystal and determine unit cell
      scan_0x_yyyy.sfrm – detailed frames used for full analysis
 
work.zip: files generated by the indexing, integration, absorption correction, and structure solution and refinement are stored
    generated by SAINT (integration) .raw, .mul, .p4p
    generated by scaling / SADABS (absorption correction) .abs, .hkl – lists each hkl index and reflection intensity
    generated / used by XPREP, SHELXS, SHELXL .ins – instruction file, .res – results file, .hkl – merged hkl file used in structure solution / refinement, .lst – listing (log) file
    generated by SHELXL .cif – crystallographic information file, contains all the information about the final structure
    image files (diagnostic) .eps, .png
 
report.zip: files needed to display a web page with the full report and a Jmol view of the structure
    generated automatically report.html – the final report
      report.jmol – the CIF (crystallographic information file) file containing all the structure information