Taking a Data Set
From marccd GUI select 'Acquire' menu and then Dataset.
A new window will appear:
In the top part of this window the user can select:
- Experiment. You can type here the file name that will characterize the experiments with the following format: root_%%_###.img where the '%%' will be used for the segment value and '###' will be used for the image number. A sample is displayed under 'Filename'. There is no default, this entry is required.
- Operator. Type here the user name. The information will go to the image header. Default is none.
- Date. Explanation needed??? The information will go to the image header.
- Comments. You can type here some comments that will go in the image header. Default is none.
- Disk Directory. This button should be ticked, and then the path for the directory to write data frames should be typed into the box. Alternatively the left mouse button can be used to select the proper directory via the browse feature.
- Archive Command. If the data is not to be processed soon, or to be stored for transport, this button can be clicked to show a tick, and an archive command can be typed into the adjacent box. Use the left mouse button can be used to select the proper directory via the browse feature. An example archive command would be tar ...
- Save video Stills. This feature allows you to capture a video still of you crystal for each frame during data acquisition.
- Multiread. This is used to remove "zingers" (cosmic rays causing spots on the frames that are not diffraction spots from the crystals). The number of sections are typed into the box to the right of this button. This option is usually desired for long exposure times (over 4 minutes).
The bottom part of this window has been designed for multiple data collection and the user can use it for data collection on a single or multiple crystals using the sample changer.
- Setting the value '0' (zero) in the Sample window means that the sample is manually mounted.
- Setting any value between '1-19' in the Sample window indicates the sample position in the carousel.
Any user willing to mount his samples manually must set the value in the sample window to zero.
The user has to select (left to right):
- Segment. In this column each individual data set is given a Segment Number. Usually one would number those sequentially starting from the top. Simply type the number into the box. This number will be included in the data file names from this Segment.
- Name. This override the filename given above.The typical format is anything_###.img where the hashes '###' are filled with the image number.
- Sample. See also explanation above. This allows the distinction between manual and automatic sample loading. Setting the value '0' (zero) in the Sample window means that the sample is manually mounted. Setting any value between '1-19' in the Sample window indicates the sample position in the carousel.
- Comment. You can type here some comments that will go in the image header. Default is none.
- Axis. Use
the left mouse button to select:
- Phi. The phi angle will scan through the oscillation range given in next to the Motion column in this table. The starting phi for each frame is automatically calculated from the starting phi of the segment and the number of frames within each Segment that have already been collected.
- Skip. No action is taken, the program will move to the next segment.
- Stop. The data collection will stop.
- Motion. Only the option Scan is given here.
- Width. Type in the width of the oscillation angle for all frames in each segment.
- Exposure time/dose. Use the mouse to choose either time (in seconds) or dose (in KHz) for the unit to define the exposure per rotation angle. Experience so far indicated that exposures longer that a minute are rarely needed. The reading from the second ion chamber on the Mar base is used to adjust the exposure time to a constant dose throughout the data set. If an exposure time of 10 seconds seems adequate at the current beam intensity, then read the current value of ion chamber 2 from the top of the main marccd window, multiply by 10 (seconds) and type the result in for 'dose'.
- Frm 1. Type the number that should be given to the first frame in each segment. Usually this is one. Do not change this value when resuming an interrupted data collection.
- NextFrm. Type in the frame number of the next frame to be collected within each segment. The first frame is usually 1 and then it increments itself. This is useful if the data collection was interrupted and should be restarted. If the interruption was accomplished via a "STOP" or "ABORT" from the marccd software, then this data collection panel is automatically updated to the proper "NextFrm". However, it is sometimes wise to change this number by hand and retake the last frame before the inturruption (i.e if the beam dumped and it is not certain that the last frame was fully exposed). If this table was not updated by the software after an interruption, then check the frames written to disk and retake the last one by entering the appropriate number here.
- Frm N. Type in the total nember of frames to be collected in each segment.
- Phi. Type in the starting angle in degrees for the first frame (Frm1).
- 2-Theta. Type in the angle in degrees for 2-Theta.
- Distance. Type in the distance in mm for the Crystal to detector distance.
- Beamstop. Type in the distance in mm for the beamstop distance.
When you have filled in all the required fields press "Check". This will check for possible conflicts in filenames, ect. When You are happy with your checking press "Start" to start data collection.
If in doubt call your station scientist
