Data Collection Mount, center and collect your crystals with SERGUI on 22-ID-D. Data Collection Using SERGUI (PDF) 1. Organizing your data Automatic folders: SERGUI creates a sub-directory for each crystal, named from the puck name and pin number. You don't need to set this up. Sample file (.xlsx): needed only for automated collection. It has five columns: Puck, Pin, Sample, Resolution, AutoCollect. Download the template from Document → Download SER-CAT Sample Template File. See Automated Data Collection. Naming rules: Puck names must match the Puck list. Puck and Sample names can't contain spaces or special characters; only - and _ are allowed. Pin must be 1–16. 2. Energy and wavelength 22-ID-D covers 6–18 keV. Each session starts at 1.00 Å. Enter the energy in eV (not keV) or as a wavelength in Å. The undulator gap reads slightly higher than the set energy. This is normal. 3. Sample mounting The robot holds up to 30 UniPucks; 20 full pucks can be set up at once. Staff load your pucks. Check their positions in the Sample tab → Puck list. After mounting, SERGUI aligns the loop automatically (Auto-loop). Wait for it to finish, then center your crystal. Defrost the gripper every 10–15 samples: Sample tab → Defrost (about 2 minutes; the button turns from yellow back to green). 4. Collecting data Type sergui in a terminal and enter your contact information. Short videos on alignment and rastering are in the Document menu. Mount and center your crystal. If you need to raster: 2D Raster: interactive. You pick positions from the raster ranking. 3D Raster: full automation only. Collect tab → Collect Single to screen. Start with 50% transmission, 0.05 s and 0.25° (50 µm pinhole), then adjust using maxPix in the KID image display. Collect tab → Collect Dataset. Collection is fast, so collect every crystal that diffracts reasonably well. Check processing results with Autoproc Log at the bottom of SERGUI. The closest detector distance is 165 mm, and the detector moves at about 1 mm/s. MAD / SAD: mount a spare crystal and take a single image to check centering. Run a fluorescence scan at low transmission and click Analyze. Check the peak, edge and remote energies before collecting. 5. Beamline tools and standards YAG crystal: beam alignment. Alignment pin: checks that the rotation axis matches the cross-hairs. Trypsin crystal (P2₁2₁2₁): in-house standard. It still diffracts well even if it looks icy Troubleshooting Blank images with no diffraction Recheck that the crystal is on the cross-hair. Ice under the pin base can melt and make the pin slip, so make sure the pin is stable before collecting. If the loop moves in the cryostream, collect in the orientations where it stays stable. No beamstop shadow? Check Ring Current and Beam Status at the bottom of SERGUI. If the beam is off, see APS Machine Status for the reason and the expected return time. The beam just came back Open the A shutter, then the D shutter, from the Help menu. Recheck the beam alignment with no sample mounted. If it's off the cross-hair, run the optimization scans on the Hutch tab. I can't see my sample Set the camera zoom to level 1 and rotate the sample 90° or 180°. If the pin base isn't seated properly, don't mount another sample. Contact staff right away, because the gripper could hit the pin. SERGUI won't open Check that you're connected to 164.54.208.73; see [NoMachine Setup]. If the terminal says you're not scheduled for data collection, contact staff. They enable access once the beamline is ready for you. Quick look at processing results In the data set's directory, type zsum -b. It summarizes results from cmdxds, Kylin and cmdDials. Results can take a few minutes to appear. Which crystals have I already mounted? See the robot usage log (mysql_robot_usage_log_<date>) in your data collection directory. KID display closed? Use Help → Start kid display.
