Data Collection
After
the beam line has been properly aligned, you have checked the sample goniometer
alignment, and you have mounted and aligned a sample, you are ready to collect
an image. The sergui collect page has 3 sub pages:
Collect Single, Collect Strategy and Collect Runs. Each of these pages has a common Archive
Section where the Sample ID or frame prefix and data archive path are defined.
The archive path should be browsed for and not entered manually to prevent
typing errors. The bottom of this document has a question
and answer section that describes how to use this page.
Collect
Single
The collect single page is used to collect single oscillation images and is shown below.
This page is divided into 5 sections:
X-ray: Used to set the wavelength/energy and attenuation for the exposure.
Detector: Used to set detector parameters: distance, offset and 2-theta.
Exposure: Used to set the exposure time and oscillation width.
Dark Image: used to collect a new dark image (not normally used as system automatically collects dark images)
Shutter: Used to toggle the timing shutter open/closed for phosphor alignment).
The frame name in this page will be defined by the sample id and number. If the sample id is set to sample, then the file name will be sample1_s.####. The frame number will be incremented with every frame. A new frame is collected when the Collect button is pressed.
A user will not normally
use the Collect Dark Image feature of this page.
This page provide two functions for the user: Its primary function is to simplify the run list generation, while its second function is to collect a limited amount of data and provide the user with a data collection strategy.
.
This page is divided into 4 sections:
Goniometer: This section is used to determine the data collection parameter: exposure time, starting angle, scan width, number of frames, and detector distance.
Wedging: This section is used to setup wedged data collection, either in angle, wavelength, or in both.
Energy: This section is used to define the data collection energy or energies in the case of a MAD experiment.
Strategy Data Collection: This section is used to setup an automated data collection and processing run, which will provide the user with a data collection strategy.
Examples on how to use this page are given at the end of this document.
The collect runs page is used to collect data sets. This page can be either manually setup (highly discouraged) or generated from the collect Strategy page (preferred). Each line represents a new data collection run. The ID number is used to keep data collected within the same wedge as a single data set, as explained in the question and answer section below.
Q: How do I Setup up a single wedge of data at 1 energy?
A: Enter parameters in the Goniometer section. Make sure
that all of the buttons in the Wedging section are pressed N. In the Energy
section, make sure that the Starting Energy has the correct value, and that the
other energy buttons are NOT checked. Once this is done, press the generate
Runlist button.
The run list on the Collect Runs page can be edited by hand.
Q: How do I setup an inverse beam experiment at a single
wavelength?
A: The only change from a single wedge of data is to press
the inverse beam button in the wedge section.
Note: 2 data sets will be generated from this data collection run. The ID number (second labeled column on the Collect Runs page) is used to differentiate the 2 different data sets: the 2 data sets will be named single_wedge1_1.#### and single_wedge1_2.####.
Q: What if my sample is radiation sensitive and I want to
collect a SAD data set wedged in angle?
A: In this case, The Collect Data Wedged in Angle must be
pressed and a value for the wedge size supplied.
Note: The system will still only provide 2 data sets for this data collection run, not the 6 that are identified in the Collect Runs page. The ID number is once agina used to append the frames onto the 2 data sets single_wedge1_1.#### and single_wedge1_2.####.
Q: What if I want to collect MAD data in inverse beam mode
wedged in Angle and Energy?
A: For this
complicated data collection strategy, the user will need to just set the
Collect Data Wedges in Energy button to yes, enter a second energy in the
Energy section and check the use in data collection button for the second
energy.
Note that in this case, the run list has 4 ID numbers identified, so the end result will be 4 data sets representing the inverse data sets at each of the 2 selected energies.
Q: So how do I collect my Data?
A: Press the Collect button at the bottom of the Collect
Runs page.
Q: Can I pause and restart the data collection?
A: Yes, after the data collection has begun, an abort button
will appear at the bottom of the Collect Runs page. Press this button and the data
collection will stop after the current frame.
Q: Can I resume my data collection after it is aborted?
A: yes, to continue with the next frame, just press the
collect button. If you want to step back some frame, then change the number in
the next field to indicate which frame you want to start on and then press the
collect button.
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