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Subsections


Getting Started

A brief introduction to Web-Ice

Web-Ice is a web browser application designed as a high-level interface to PX experiments at synchrotron beamlines. Web-Ice can be used to access screening and autoindexing results 24/7, remotely or locally.

In addition, Web-Ice can be used during beamtime to monitor the beamline instrumentation and control panel via the beamline video system, view diffraction images as they are collected, and calculate and set up a data collection strategy in a semi-automated fashion (the user gets to review and, if desired, edit the strategy before initiating data collection). Web-Ice is totally synchronized and can be used simultaneously with Blu-Ice.


References

The main reference to Web-Ice is: A. González, P. Moorhead, S. E. McPhillips, J. Song, K. Sharp, J. R. Taylor, P. D. Adams, N. K. Sauter and S. M. Soltis. ''Web-Ice: integrated data collection and analysis for macromolecular crystallography.'' J. Appl. Cryst. 41, 176-184 (2008).

External software used by Web-Ice include:

  • SPOTFINDER/DISTIL (diffraction spot location and image analysis): Z. Zhang, H. van den Bedem, N. K. Sauter, G. P. Snell and A. Deacon J. Appl. Cryst. 39, 112-119. (2006).

  • LABELIT (autoindexing): N. K. Sauter, R. W. Grosse-Kunstleve, and P. D. Adams. J. Appl. Cryst. 37, 399-409. (2004)

  • MOSFLM (data integration and overlap analysis): A. G. W. Leslie; in Crystallographic Computing, Oxford University Press. (1990)

  • BEST (exposure time calculation and, since May 2008, oscillation range): A. N. Popov and G. P. Bourenkov. Acta Cryst. D59, 1145-1153. (2003)

  • RADDOSE (absorbed dose calculation): J. W. Murray, E. F. Garman and R. B. G. Ravelli. J. Appl. Cryst. 37, 513-522. (2004)

  • XDS (data processing): W. Kabsch, Acta Cryst. D66, 125-132. (2010)

  • The CCP4 programs SCALA, TRUNCATE, MOLREP, REFMAC (for data processing, scaling, analysis, structure solution and refinement): Collaborative Computational Project, Number 4. Acta Cryst. D50, 760-763. (1994)

  • XTRIAGE (data quality assessment): P. H. Zwart, R. W. Grosse-Kunstleve and P. D. Adams CCP4 newsletter 43. (2005)

For additional information about the Web-Ice project please see
http://smb.slac.stanford.edu/research/developments/webice/.

What is needed to run Web-Ice?

  • You need an account on the SSRL Macromolecular Crystallography computers. New accounts can be requested by fooling the instructions at
    http://smb.slac.stanford.edu/facilities/computing/account.html

  • Your data needs to be stored in the SSRL MC file system (default when collecting data at the MC beamlines). The system does not support image download from remote computers.

  • Some software in Web-Ice uses information from the image header , in order to reduce the need for user input; this means that only SSRL collected images are actively supported by the software.

  • The browser must be set to accept cookies in order to log in to the Web-Ice application.

  • Javascript should be enabled in the browser in order to have access to all the Web-Ice features.

Supported browsers

The Web-Ice interface has been optimized for Firefox (v. 1.5 or newer); and Internet Explorer (v. 6 or newer). Since May 2007, the javascript applications work under Safari.

How to start Web-Ice

  1. Launch a browser window from any computer and enter the URL
    https://smb.slac.stanford.edu/webice/ChangeTab.do?tab=welcome

  2. Log in using your SSRL computer account name and password. You will be directed to a Welcome page containing a very brief description of the Web interface and instructions to connect to a beamline or obtain on-line help. The page displayed on log-in can be changed by the user.

There are also links to Web-Ice in the Blu-Ice GUI. Authentication is not required when logging in through Blu-Ice.

Web-Ice Interface

The Web-Ice applications are grouped by function under several menus or Tabs, displayed at the top of the Web-Ice window. By clicking on the tabs, the user links to pages providing access to the different functions:

  • Image Viewer: This tab directs the user to the diffraction image analysis tools interface. Here, the user can inspect diffraction images and spot statistics.

  • Autoindex: This tab provides tools to collect test images (optional), autoindex, calculate a strategy for the experiment and collect a full monochromatic, MAD or SAD data set.

  • Process: This tab runs a workflow to process, analyze, scale and merge data, and optionally, to attempt structure solution by molecular replacement.

  • Screening: The Screening tab provides an interface to the the automated screening results. Tools to easily identify the best samples for data collection are provided.

  • Beamline: Access to different beamline monitoring tools.

  • Video: From the video tab, the user has access to the beamline video cameras set up to monitor the experiment.

  • Preferences: The Preferences tab shows the user information and permissions and system and user set preferences for the session.

The user can select a beamline using the drop-down menu on the top bar and clicking the Select button. When a beamline is selected, the user can view the images as they collected, as explained in the Image Viewer section. Selecting a beamline is required to calculate a data collection strategy specific to the beamline in question, as described in the the Autoindex Tab help, and to access the beamline video feed.

Figure 1: Detail of the Web-Ice interface window showing the Beamline Selection tool and links to log out and the on-line documentation.
Image blselect

Clicking the Log out button exits Web-Ice. The user will have to log in again in order to continue using Web-Ice. The connection to the web server will also be reset if Web-Ice is left idle for 30 minutes.

To access the on-line Web-Ice documentation, click on the Help link at the right of the Web-Ice window. This will open a new browser window with specific information on the tab the user is currently visiting.

New features

2017

  1. Automated data processing implemented at some beamlines.

2015

  1. Strategy determination has been further streamlined for speed. The selection of the program ''MOSFLM'' or ''BEST'' is done automatically.
  2. When the user provides the number of anomalous sites and number of residues, the program uses the information to calculate the strategy for MAD and SAD experiments.

2014

  1. When the crystal point group (``Laue group'') is provided by the user (via drop down menu) the data collection strategy is only calculated for that particular symmetry. This cuts down the calculation time considerably.

2013

  1. Multicrystal strategy calculation option in the autoindex tab. Useful for microcrystals, room temperature data collection and samples particularly sensitive to radiation damage.

2012

  1. Faster preparation for data processing.

  2. If the space group is provided as input to strategy calculation, the strategy will only be computed for P1 and the given space group. This can save some time for high symmetry groups.

2011

  1. Implementation of a data processing and structure solution tool based on an Autodrug workflow.

  2. New button to recalculate the dose when a different number of images or crystal exposure is selected before exporting the strategy to Blu-Ice.

2010

  1. Supporting strategy calculation for the PILATUS 6M detector; thin phi slices are used with this detector.

2009

  1. Increased data multiplicity for MAD and SAD experiments.

  2. Using the latest version of RADDOSE (2008). This version gives a better estimate of the absorbed dose for higher energies.

  3. An optimal exposure time is calculated for each space group.

2008

  1. Generation of an executable shell script to re-run RADDOSE manually.

  2. The screening results are updated automatically by default. If the user prefers not to have automated updates, they can turn off this feature in the Preferences tab. The update button still works in either case.

  3. BEST can used instead of MOSFLM to calculate the oscillation range (total and per image). The MOSFLM strategy TESTGEN option is always used to carry out the spot overlap analysis over the entire range of rotation.

  4. The beam may be attenuated for collection of the test images used to calculate the data collection strategy. The attenuation defaults to the value currently set at the beamline.

  5. For MAD and SAD experiments, it is possible to declare the number of heavy atoms in the molecule. This results in a more realistic estimate of the absorbed dose. Also, the dose is taken into account to calculate a data collection wedge size.

2007

  1. Extensive revamping of the Web-Ice interface to facilitate navigation.

  2. Reorganization of files in the webice/autoindexing directory to make it easier for users to locate the Web-Ice input command files and logs used for strategy calculation.

  3. Improved image mark-up in the Image Viewer and Screening Cassette Details pages. The same diffraction image application is also used to display the Autoindex Predictions (replacing the old Java tool)

  4. javascript applications have been modified to run under Safari.

  5. An improved BEST version (3.1) is used to calculate the exposure time.

  6. Several bugs in the strategy calculation have been fixed.

  7. Possibility to select any element from P to U for non-optimized SAD experiments.

  8. It is no longer required to select an experiment type if the strategy calculation is not requested.

  9. For MAD experiments, the absorbed dose at each energy is given. If the total absorbed dose for three energies exceeds the Garman limit, only two energies will be used for data collection.

2006

  1. Fluorescence scan collection and automated full MAD and SAD strategy calculation can be carried out from the Autoindex Tab

  2. Beam attenuation is automatically calculated and included in the data collection strategy when the exposure time calculated by BEST is small.

  3. The resolution limit calculated by LABELIT is used in for image integration. This results in fewer autoindex error for low resolution images.

  4. Automated test image collection implemented in the Autoindex tab.

  5. The user may supply a specific Laue group and unit cell as input to autoindexing (Autoindex setup page). The default data collection strategy is given for this space group.

  6. The user may configure the image viewer application to perform automated analysis of the image with SPOTFINDER. The option is set in the Preferences Tab.

  7. The crystal score is calculated and displayed when autoindexing using the Autoindex Tab.

  8. Selection of a data collection strategy to maximize anomalous pairs has been enabled in the strategy page (Autoindex Tab).

  9. Video monitoring of the beamline available from the Video Tab.

  10. Improved strategy calculation using BEST and RADDOSE.

  11. Possibility to export the strategy to Blu-Ice/DCS.

  12. Updates for LABELIT and SPOTFINDER result in a more robust autoindexing.