Next: Troubleshooting
Up: Web-Ice
Previous: Beamline status
Subsections


Preferences

The Preference tab can be used by the user to edit several options affecting how and when the data are displayed by Web-Ice.


Saving the Preferences

The values entered by the user in the Configuration table will be valid the first time the user visits the different Web-Ice tools. If the user then selects different options while running Web-Ice, the values in the preferences will be updated. To preserve the initial values, the user must click the Save button at the bottom of the Configuration Options selection menu.


General Configuration

Figure 32: General configuration options.
Image pref-conf1

  • Global Image Directory: This will be the starting directory to browse the user directories for the input image files.

  • Image Filters: Used to specify what files are to be displayed by the directory browser. This makes it easier to find types of a certain type. Multiples entries separated by a blank space are accepted; for example: ''*.img *.mccd *summary''.

  • Show Welcome Page: Set to no to stop seeing the Welcome page upon login to the Web-Ice interface.

  • Default Tab: Select the tab to be displayed upon login to the Web-Ice interface.


Image Viewer Configuration

Figure 33: Image Viewer configuration options.
Image pref-conf2

  • Use Global Image Directory: When this is set to Yes, the Image Viewer will use the directory specified in the General Configuration as starting point for image file browsing. If it is set to No, a specific Image Directory may then be given. The Image Directory will be updated every time the user selects an image for display with the Image Viewer.

  • Show Overlay Spots: If this option is set to Yes, the Image Viewer will display the SPOTFINDER generated image highlighting the spot positions, ice rings and resolution limit. This option should only be set to Yes in conjunction with the next option Automatically Analyze Image.

  • Automatically Analyze Image: When set to Yes, the Image Viewer will automatically run SPOTFINDER on the selected image. If set to No the user must click the Analyze Image button in the Image Viewer tab to analyze a specific image.


Autoindex Configuration

Figure 34: Autoindex configuration options.
Image pref-conf3

  • Use Global Image Directory: When this is set to yes, the Autoindex Viewer will use the directory specified in the General Configuration as starting point for image file browsing. If it is set to no, a specific Image Directory may then be given.

  • Number of runs per page: This sets the maximum number of runs which will be loaded and displayed on a single page in the All Runs frame. It is recommended to keep this number below 20, as loading a large number of runs simultaneously may cause performance problems.

  • Reverse Autoindex Log: When set to yes, the Autoindex Log displays messages in inverse chronological order, i.e., the latest message appears at the top of the log.

  • Reverse DCSS Log: When set to yes, the Beamline Log displays messages in inverse chronological order, i.e., the latest message appears at the top of the log.

  • Automatically Update Run Log: When set to yes, the autoindex log in the Selected Run Log page will be automatically updated as the autoindexing and strategy calculating programs run. If not, an update button will appear on the log.


Screening Configuration

Figure 35: Screening configuration options.
Image pref-conf4

  • Automatically Update Screening Output: If set to yes, the screening results will be refreshed automatically in the Cassette Summary, and a link to the results will be generated in the Cassette details.

  • Update Rate (sec): How frequently the screening results are updated. This only applies if the Automatically Update Screening Output option is set to ''yes''.

  • Column Display Options: This can be used to select the columns displayed in the Cassette Summary:

    • Original: Displays only the columns present in the user's spreadsheet.

    • Minimum: Displays the cassette port number, crystal ID, protein name and the comment column.

    • Results: Displays the same columns as the Minimum display plus the columns containing the screening results (generated by the screening software).

    • All: Displays the original spreadsheet and the results columns.

  • Image Display Options: These options determine the information shown in the Images column of the Cassette Summary.
    • Hide images: Displays only the image name.

    • Show Image links only: Displays the results of the diffraction image analysis for the images collected at different crystal orientations during screening and links to the diffraction image and crystal snapshots. Clicking on the links opens a window displaying a JPEG file.

    • Selected Sample only: Displays the results of the image analysis and diffraction image and crystal snapshot JPEGs for the sample selected by the user.

  • Crystal Sorting Column: By default, the samples will be sorted by the column selected in this option.

  • Crystal Sorting Direction: By default, the samples will be sorted in the order (ascending or descending) selected in this column. For example, if the Crystal Sorting Column is ''Score'', and the Crystal Sorting Direction is ''Descending'', the highest scoring samples will be displayed first.


Video Configuration

Figure 36: Video configuration options.
Image pref-conf5

  • Displayed Camera: This option controls what video feed is displayed by default in the Video page. Selecting All will display all video feeds. If the user's bandwidth is limited, it may be more advantageous to display one video feed at one time.

  • Camera Update Rate: The user may choose how often (in seconds) the video refreshes the image for each camera. Shorter times provide a more smooth live video, at the expense of bandwidth usage.