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Subsections
Getting Started
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/.
- 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.
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.
- Launch a browser window from any computer and enter the URL
https://smb.slac.stanford.edu/webice/ChangeTab.do?tab=welcome
- 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.
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.
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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.
- Automated data processing implemented at some beamlines.
- Strategy determination has been further streamlined for
speed. The selection of the program ''MOSFLM'' or ''BEST'' is done
automatically.
- 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.
- 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.
- Multicrystal strategy calculation option in the autoindex
tab. Useful for microcrystals, room temperature data collection and
samples particularly sensitive to radiation damage.
- Faster preparation for data processing.
- 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.
- Implementation of a data processing and structure solution tool
based on an Autodrug
workflow.
- New button to recalculate the dose when a different number of images or
crystal exposure is selected before exporting the strategy to Blu-Ice.
- Supporting strategy calculation for the PILATUS 6M detector;
thin phi slices are used with this detector.
- Increased data multiplicity for MAD and SAD experiments.
- Using the latest version of RADDOSE (2008). This version gives a
better estimate of the absorbed dose for higher energies.
- An optimal exposure time is calculated for each space group.
- Generation of an executable shell script to re-run RADDOSE manually.
- 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.
- 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.
- 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.
- 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.
- Extensive revamping of the Web-Ice interface to facilitate navigation.
- 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.
- 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)
- javascript applications have been modified to run under Safari.
- An improved BEST version (3.1) is used to calculate the exposure
time.
- Several bugs in the strategy calculation have been fixed.
- Possibility to select any element from P to U for non-optimized
SAD experiments.
- It is no longer required to select an experiment type if the
strategy calculation is not requested.
- 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.
- Fluorescence scan collection and automated full MAD and SAD
strategy calculation can be carried out from the Autoindex Tab
- Beam attenuation is automatically calculated and included in the
data collection strategy when the exposure time calculated by BEST is small.
- The resolution limit calculated by LABELIT is used in for image
integration. This results in fewer autoindex error for low resolution images.
- Automated test image collection implemented in the
Autoindex tab.
- 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.
- 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.
- The crystal score is calculated and displayed when autoindexing
using the Autoindex Tab.
- Selection of a data collection strategy to maximize anomalous
pairs has been enabled in the strategy page (Autoindex Tab).
- Video monitoring of the beamline available from the Video Tab.
- Improved strategy calculation using BEST and RADDOSE.
- Possibility to export the strategy to Blu-Ice/DCS.
- Updates for LABELIT and SPOTFINDER result in a more robust
autoindexing.
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