Eppley Institute for Cancer Research
University of Nebraska Medical Center
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Eppley Institute for Cancer Research |
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University of Nebraska Medical Center |
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The tools menu provides a list of functions designed to make it easier to export information out of BEAM-ish for use in papers or other tools.
The following will describe each what each option does.
The renumber images command will analyze the fine phi image sequence based on the image prefix. The image prefix is set in under the project settings dialog box. It will order the images based on the phi angle as stored in the header. It will then sequentially rename all of the images.
This function was originally implemented to recover image data from a fine phi set that was larger than 1000 images. The ADSC software comes up with very creative names when the image count goes greater than 1000. When completed the software will produce a file that shows what the original name was and what the new name is. The file is called "RenameList.txt" and is stored in the project directory. It is formatted with one line for each file as "OriginalFileNameAndPath AngleFromHeader NewFileNameAndPath"
If the fine image exist then simply select this command from the menu.
This command can not be undone.
The Save Raw Detector Image will save the detector as a TIFF file with colors mapped to the current legend. The TIFF will be saved with bands encoded by the LZW algorithm to save space on the disk. The is a lossless compression technique.
When the command is selected BEAM-ish will prompt the user for the name of the file.
The Save Screen Detector Image will save the image of the detector how it currently appears on the screen. For example if the reflections are high lighted then the image saved image will have them highlighted also. This image is scaled to 1/2 or 1/4 original size when it is saved because that is how it is drawn on the screen. The TIFF is saved with LZW band compression.
When the command is selected BEAM-ish will prompt the user for the name of the file.
The Save Zoom Window Image will save the zoom window as it currently appears. Since the zoom window follows the mouse the only way to capture a zoom image of a reflection is to center the mouse over the reflection and then activate this command with the keyboard. The TIFF is saved with LZW band compression.
When the command is selected BEAM-ish will prompt the user for the name of the file.
The Save Screen command will save the entire Main Window to a TIFF image file. The TIFF is saved with LZW band compression.
When the command is selected BEAM-ish will prompt the user for the name of the file.
The Save Animation command generate two sequences of TIFF images. The first will be the a sequence that contains the all of the frames in the animator. The second sequence will include a sequence of the profile graph with the bar at each location. In the lower right hand corner the proper frame from the animator will be overlaid on the profile graph.
The animator files are named with the following convention as indicated by this example:
actin5_2_h5k4l-32104.tif
ProjectPrefix + h + h index value + k + k index value + l + l index value + ### + .tif
where ### is the frame number
The profile files are named with the following convention as indicated by this example:
PIactin5_2_h5k4l-32104.tif
PI + ProjectPrefix + h + h index value + k + k index value + l + l index value + ### + .tif
where ### is the frame number
These TIFF files are all saved with LZW band compression.
This command was used to generate the animations that are seen on the http://sbl.unmc.edu website under the crystal perfection research section.
The Save Profile As Text command will write the current profile to a text file that can be imported in to a variety of other applications.
This command will prompt the user for the name of the file. The format of the file is described in RefPro*.txt section.
The Mark Sym Rel Refs command is used to have BEAM-ish search for all the symmetry related reflections. If IPC is not enabled then the search set will be limited to the reflections in the current project. If IPC is enabled then the search set will include all the projects in the server list and the current project. After the command runs it will have a check mark by it indicating that the operation is complete.
If the command is run when it has a check mark by it then all the symmetry related reflection information will be dumped.
The Generate Master Report command will cause BEAM-ish to write one large file containing all of the reflection data including symmetry related reflection information. If IPC is enabled then this command will compile a file for all reflection data across all open projects in the server list.
When run between multiple projects only the project that initiated the Mark Sym Rel Refs command will have this option enabled. This is due to the random nature in which project ID's are generated and the values would not be valid if this command were called from another instance. Additionally, a extra file is generated which contains mapping information from project ID's to project names.