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SMART X2S User Manual Part Number: DOC-M86-EXS127 V4 Publication Date: 25 March 2011 SC-XRD Innovation with Integrity...
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Bruker AXS Inc. nor the rights of others. Bruker AXS Inc. does not assume any liabilities arising out of any infringements of patents or other rights of third parties. Bruker AXS Inc. makes no warranty of any kind with regard to this material, including but not limited to the implied warranties of merchantability and fitness for a particular purpose.
About this User Manual The Structure of this User Manual This User Manual describes the SMART X2S and its functions, and illustrates the steps required to perform a structure determination: • Introduction to the SMART X2S describes the system, its specifications, and its functions;...
“X”. Always use the most current revisions available. All of the documents shown in the Table may be found at Bruker AXS’ comprehensive support site www.brukersupport.com, or on the Online Documentation CD-ROM that accompanies the shipment.
SMART X2S User Manual About this User Manual Terms and Conventions 1.3.1 Equivalent Terms Frame/Image In 2-dimensional X-ray diffraction, the terms frame and image refer to the same 2-dimensional view of the diffraction pattern. Greek and Roman Text This document uses scientific terminology that may be rendered in Greek text. However, this document follows a convention of using Roman text to the greatest extent possible.
The SMART X2S is intended for benchtop use only. The SMART X2S may only be used for the applications specified in its User Manual or Specification Sheet, and only in conjunction with devices or components from other manufacturers that have been approved or recommended by Bruker AXS.
When the switch is off (i.e., “0” is in the depressed position), no power is being supplied to the SMART X2S. When the switch is on (i.e., “1” is in the depressed position), power is being supplied to the SMART X2S and the switch is illuminated green.
About this User Manual SMART X2S User Manual 1.4.4 X-ray Safety DANGER WARNING X-ray equipment produces potentially harmful radiation and can be dangerous to anyone in the equipment’ s vicinity unless safety precautions are completely understood and implemented. All persons designated to operate or perform...
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SMART X2S User Manual About this User Manual Continuous Spectrum When accelerated electrons collide with atoms in the metal target, they can be stopped on impact (in which case all their energy is converted into radiant energy), or they can be decelerated in steps (in which case a part of their total energy is released in the form of X-rays of greater wavelengths at each step until it is expended).
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About this User Manual SMART X2S User Manual Characteristic Spectrum High-energy electrons can also interact with the atoms of the metal target to produce another type of radiation called “characteristic” radiation because the wavelengths of the photons emitted are characteristic of the anode metal.
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SMART X2S User Manual About this User Manual In fact, on closer examination of the atom and its electron shells, it can be seen that the shells are divided into subshells as shown in Figure 1.5 below. For this reason, K radiation can be divided into...
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About this User Manual SMART X2S User Manual In Figure 1.6 below, the wavelength distribution of both continuous and characteristic radiation is shown as a function of intensity or the number of pulse counts per second. The characteristic peaks K and K are clearly visible above the continuous spectrum.
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SMART X2S User Manual About this User Manual Biological Effects of X-Rays Mechanisms of Damage Injury to living tissue results from the transfer of energy to atoms and molecules in the cellular structure. Ionizing radiation causes atoms and molecules to become ionized or excited. These excitations and ionizations can: •...
Disposal of beryllium must comply with all applicable national, state, and local regulations. 1.4.6 Perchlorate Safety The SMART X2S uses a lithium coin battery that contains perchlorate, a hazardous material. Disposal of perchlorate must comply with all applicable national, state, and local regulations. 1 - 12...
Figure 1.7 — Help button 1.5.2 Technical Support from Bruker Service Centers You are invited to contact Bruker AXS whenever there are problems or questions related to the system. Before contacting Bruker AXS, please: • Have the system’ s serial number available;...
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About this User Manual SMART X2S User Manual Karlsruhe Service Center Contact Information Table 1.5 — Bruker AXS Karlsruhe Service Center contact information Bruker AXS Karlsruhe Service Center Bruker AXS GmbH Customer Support Address: Östliche Rheinbrückenstr. 49 76187 Karlsruhe Germany...
For more information about the theory behind the SMART X2S, refer to Bruker AXS’ Application Note A86-Exx003 Fundamentals of Single Crystal Diffraction. Before using your SMART X2S, check that it is properly installed and in proper working order (e.g., that the touch-screen interface appears when the system is powered up).
CAUTION WARNING It is important to be able to easily disconnect the SMART X2S from mains power in the event of an emergency or for service. Do not position the SMART X2S such that it is difficult to disconnect from the mains power supply.
Environment Requirements Horizontal tabletop, countertop, or other stable, vibration-free surface rated for the Installation surface weight of the SMART X2S. For additional stability, the SMART X2S may be bolted to the installation surface. Heat dissipation less than 300 W (1024 btu/hr) Clearance behind at least 3”...
2.4.1 Starting Up the SMART X2S Some SMART X2S units have a safety key switch that must be unlocked before the system can be turned on. If you have a safety key switch, turn it to the “On” position. Press the power switch on the front panel to the “On” position.
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Introduction to the SMART X2S SMART X2S User Manual Then, the instrument starts GIS, the control software for the SMART X2S hardware. Figure 2.6 — Starting GIS After the system finishes initializing, it begins cooling the detector and desktop cooler (if present).
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SMART X2S User Manual Introduction to the SMART X2S After cooling is complete, the kiosk-style interface appears. Figure 2.8 — Starting kiosk application Finally, the system checks whether a sample is loaded. If a sample is loaded, the instrument will eject the sample and make it available at the sample port. If no sample is loaded, the instrument will display the “Welcome”...
Shutting Down the SMART X2S Flip the power switch on the front of the SMART X2S to the “Off” position (“0”). If your SMART X2S unit has a safety key switch, turn it to the “Off” position and remove it to prevent unauthorized access.
Sample Preparation and Mounting To study a sample with the SMART X2S, the sample must be mounted on a Bruker Spine Pin. Sample Preparation Overview The process of sample mounting is simple: from the many crystals within a bulk sample, identify the best candidate for study and affix it to the Bruker Spine Pin with a special ultraviolet-curable adhesive.
The Bruker Spine Pin uses a MiTeGen MicroGripper™, precision-manufactured to work properly within the SMART X2S. The Pin has a magnetic cap that protects the sample. The crystal needs to be attached across the crystal aperture at the tip of the MicroGripper™.
SMART X2S User Manual Sample Preparation and Mounting Sample Preparation Procedure 3.3.1 Identifying Suitable Crystals Begin by using the microscope to look for a suitable crystal in the bulk sample. The ideal crystal should • Uniform in color; • Free of cracks and inclusions;...
Sample Preparation and Mounting SMART X2S User Manual 3.3.2 Separating the Crystals Isolate suitable crystals from the bulk sample, and move them to a separate area on the microscope slide. Compare the crystals, and choose the best one. Figure 3.5 — Candidate crystals, separated from bulk sample 3.3.3...
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SMART X2S User Manual Sample Preparation and Mounting NOTE: The adhesive can be used to “wash” crystallites from the surface of the candidate crystal. Be careful that the flowing adhesive does not carry the crystal out of the microscope’ s field of view.
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NOTE: Make sure that the crystal is in the aperture. If the crystal is not in the aperture, the SMART X2S may not be able to collect data. Figure 3.9 — MicroGripper™ near desired crystal Figure 3.10 —Crystal in MicroGripper™ aperture...
20 seconds. Figure 3.11 — Adhesive illuminated by ultraviolet pen light When the adhesive is cured, place the Bruker Spine Pin in its protective cap. The sample is now ready for use with the SMART X2S.
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Setting Up Data Collection The SMART X2S Touchscreen Interface The SMART X2S features an intuitive, kiosk-style interface with input through a touchscreen. The interface guides the user through the experiment, providing easy-to-understand graphical feedback about the status and quality of the structure determination process.
After touching the “Welcome” screen, the “Please insert an empty CD” screen appears. Figure 4.2 — Please insert an empty CD Insert an empty CD, label side up, into the slot on the front of the SMART X2S. NOTE: The SMART X2S has no known issues with any CD-R media types.
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SMART X2S User Manual Setting Up Data Collection Figure 4.3 — Inserting a CD After the SMART X2S recognizes that an empty CD has been inserted, a confirmation screen will appear. Figure 4.4 — Confirmation screen The SMART X2S automatically proceeds to the “Please name your compound” screen.
Figure 4.5 — Please enter the sample name Use the keyboard on the touchscreen to name the compound. This is the name that will be used in the report generated by the SMART X2S. NOTE: The compound name is limited to a maximum of 12 characters.
SMART X2S User Manual Setting Up Data Collection Entering the Sample Formula After naming the compound, the “Please enter the sample formula” screen appears. Figure 4.7 — Please enter the sample formula Use the periodic table’ s element buttons to enter the sample formula.
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Setting Up Data Collection SMART X2S User Manual NOTE: The SMART X2S will learn the 8 most frequently-used elements and display them in a bar along the top of the periodic table. If the formula is present and valid, a green check mark will appear in the lower right-hand corner of the screen.
Specifying the Crystal Color After entering the sample formula, the “Please specify the crystal color” screen appears (the color will be used in the report generated by the SMART X2S). Figure 4.10 —Please specify the crystal color Simply press the appropriate button on the touchscreen to choose the color.
Setting Up Data Collection SMART X2S User Manual Specifying the Crystal Shape After specifying the crystal color, the “Please specify the crystal shape” screen appears. Figure 4.12 —Please specify the crystal shape Choose the appropriate shape by pressing one of the shape buttons.
SMART X2S User Manual Setting Up Data Collection Specifying the Crystal Size After specifying the crystal shape, the “Please specify the crystal size” screen appears. Figure 4.14 —Please specify the crystal size Use the touchscreen controls to set the dimensions of the crystal.
Setting Up Data Collection SMART X2S User Manual Selecting the Redundancy Mode After specifying the crystal size, the “Please select the redundancy mode” screen appears. Figure 4.16 —Please select the redundancy mode Use the touchscreen controls to select the redundancy mode for the data collection: The button on the left (activated by default) chooses standard redundancy •...
After specifying the crystal size, the SMART X2S prompts for the sample. Figure 4.17 —Please insert your sample to begin processing Insert the sample vial into the sample port on the front of the SMART X2S. NOTE: Leave the protective cap on the sample when inserting it.
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5.1.3 Detector Frame Display While collecting data, the SMART X2S displays the current detector frame in the upper right-hand corner of the screen. Touch the frame to exchange the positions of the Detector Frame and Time Displays, providing a larger view. To return to the original view, simply touch the Time Displays.
• Generating Report. As the SMART X2S proceeds through the experiment, it moves sequentially through these steps. Each step has a status icon (Table 5.1) that shows the SMART X2S level of success in performing that step. Table 5.1 —...
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SMART X2S User Manual Data Collection and Structure Solution Checking Quality The SMART X2S begins by collecting data to determine the orientation matrix and evaluating the mosaicity of the crystal. Figure 5.4 — Checking quality Acquiring Data After indexing the unit cell and finding a suitable maximum resolution, data collection begins. The SMART X2S integrates the data, scales it, and determines the Laue class during data acquisition.
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The results are then verified against International Union of Crystallography standards. Figure 5.6 — Finding structure Generating Report After the structure determination, the SMART X2S generates the report that will appear on the CD. The report can be previewed prior to burning the CD. Figure 5.7 — Generating report...
Aborting Data Processing If you touch the button while collecting or processing data, the SMART X2S will stop. After the system has stopped, choose whether to delete the collected data, or write it to the CD. Figure 5.8 — “Data Processing Aborted” screen If you choose to delete the collected data, the system deletes the data and returns to the “Welcome”...
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Structure View, Report Display, and CD Burning Structure View After refining the structure and generating the report, the SMART X2S displays the structure in a 3D view that can be manipulated by simply touching the touchscreen. The structure appears in standard CPK colors.
Structure View, Report Display, and CD Burning SMART X2S User Manual 6.1.1 Structure View Button Functions Table 6.1 — Structure View button functions (left side) Button Function Zoom in — Zoom into display less of the structure. Zoom out — Zoom out to display more of the structure.
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SMART X2S User Manual Structure View, Report Display, and CD Burning Table 6.2 — Structure View button functions (right side) Button Function Atom labels visible — Turn atom labels on. Atom labels hidden — Turn atom labels off. Pipes display — Display the structure as pipes.
Structure View, Report Display, and CD Burning SMART X2S User Manual Report Display After the “Structure View” screen, the SMART X2S displays the report that will be burned to the CD. Figure 6.2 — Report display After examining the report: •...
Removing the CD and Sample When CD burning is complete, the SMART X2S will eject the CD. The sample will also appear at the sample port on the front of the SMART X2S. A screen appears prompting to remove the CD and sample.
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The Data CD The Crystallographic Report When the data CD is inserted into a computer with a CD-ROM drive, the crystallographic report automatically opens in your default web browser. The report contains four sections: • Report Summary • Molecule Viewer •...
Unit cell parameters, space group, and Z-value; • Structure parameters and results (integration, absorption correction, least squares, and electron density); and • Version information for the various software modules used inside the SMART X2S. Figure 7.1 — Report summary section 7 - 2 DOC-M86-EXS127 V4...
SMART X2S User Manual The Data CD 7.1.2 Molecule Viewer Section The molecule viewer allows for inspection of the structure. The molecule can be rotated and displayed in various modes (e.g., ball-and-stick, space-filling CPK model, molecule surface), and bond lengths, angles, and torsions can be measured.
The Data CD SMART X2S User Manual 7.1.3 Detailed Report Section Crystal Data and Structure Refinement Figure 7.3 — Crystal data and structure refinement 7 - 4 DOC-M86-EXS127 V4...
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SMART X2S User Manual The Data CD Atomic Coordinates and Isotropic Displacement Parameters Figure 7.4 — Atomic coordinates and isotropic displacement parameters Bond Lengths and Angles Figure 7.5 — Bond lengths and angles DOC-M86-EXS127 V4 7 - 5...
Figure 7.6 — Anisotropic displacement parameters Hydrogen Coordinates and Isotropic Displacement Parameters Figure 7.7 — Hydrogen coordinates and isotropic displacement parameters 7.1.4 Alerts Section Below the Detailed Report section is a list of alerts generated by the SMART X2S. 7 - 6 DOC-M86-EXS127 V4...
The Data CD Using the Data CD with APEX2 The data CD is designed to work with APEX2. To use the SMART X2S data CD with APEX2: Insert the data CD into the computer’ s drive. If you have a sample open in APEX2, close it.
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The Data CD SMART X2S User Manual Click Restore Archive. A progress bar and status data are shown as the software restores the archive. Figure 7.8 — “Restore Archived Sample” window (“From CD” selected) When the archive is restored, it can be opened from the Sample > Open...Sample >...
Administrator Key and Accessories Kit Administrator Key The Administrator key is shipped with the SMART X2S. It allows access to the interior of the instrument, including the storage compartment and computer drawer in the lower portion of the unit. NOTE: One individual should be designated as the “SMART X2S instrument...
Open the lower drawer by holding it along its edges, pulling up slightly (to make sure that the drawer does not bind against the surface the SMART X2S is sitting on), and pulling outward. Figure 8.2 — Lower drawer open...
CAUTION WARNING Opening or closing the SMART X2S’ hinged upper cover creates a pinch hazard. Be aware of this hazard whenever the upper cover is raised. Figure 8.3 — Hinged upper cover open 8.1.3...
SMART X2S User Manual Moving the SMART X2S 8.2.1 Moving the SMART X2S over Short Distances When moving the SMART X2S over short distances: • Make sure that the system is powered down and unplugged; • Make sure that the system’ s path is clear from its current location to its destination;...
Attaching the Outriggers Elevate the SMART X2S (e.g., on a cart), to allow access to the right and left sides of the bottom of the unit. The sides have screw holes that will be used to attach the wooden “outriggers”...
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The SMART X2S’ wooden outriggers attach to the shipping skid with four 9/16” bolts. Position the skid so that the SMART X2S can be moved onto it as easily as possible (the skid does not have a special front/back orientation).
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SMART X2S User Manual SMART X2S Administrator Information Dressing the SMART X2S for Shipping After the SMART X2S is securely attached to the skid, add the protective plastic cover and additional components. Slide the protective plastic cover over the SMART X2S.
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SMART X2S Administrator Information SMART X2S User Manual Include any extra items to be shipped with the SMART X2S by bagging them and placing them along the top of the unit (these may include the Accessory kit, the USB keyboard, and any documentation).
Four bolts attach the SMART X2S’ two wooden “outriggers” to the skid. Remove them. Install the carrying handles by inserting them and rotating them to their locking positions. Raise the SMART X2S and turn it 90°, so that the two “outriggers” are elevated off the ground.
8.3.1 Cleaning the SMART X2S The SMART X2S’ exterior panels may be cleaned with a damp cloth. Do not use soap or aggressive cleansing agents. In order to avoid damage to the touchscreen, the use of sharp objects such as styluses should be avoided.
SMART X2S Administrator Information 8.3.3 Surveying the SMART X2S for Radiation Leakage The SMART X2S should be surveyed for radiation leakage and stray radiation as a closed-beam X-ray diffraction system in accordance with the following documents: • Guide for submission of information on Analytical X-ray Equipment required pursuant 21 CFR 1002.10.
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SMART X2S Administrator Information SMART X2S User Manual Radiation Leakage Close the shutter. Survey the entire tube housing with the Geiger counter at a distance of 50 mm from the surface of the tube housing to determine areas of high intensity radiation emission.
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X-ray shutter in any other way unless specifically directed by Bruker AXS personnel. Survey the entire SMART X2S cabinet with the Geiger counter at a distance of 50 mm from the surface to determine areas of high intensity radiation emission.
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SMART X2S Administrator Information SMART X2S User Manual System Cabinet Radiation Survey Form 8 - 14 DOC-M86-EXS127 V4...
The SMART X2S’ Archival and Deletion Routine The data CD, burned at the end of data collection, is a copy of a folder on the SMART X2S’ internal hard drive. An instrument administrator can easily retrieve any sample in the SMART X2S’ history of operation—until the hard drive becomes nearly full.
Connect the Computer to the SMART X2S The preferred method of remote access to the data on your SMART X2S’ hard drive is to use an isolated/private network configuration. This consists of a computer with two separate network cards, a router with DHCP, and the SMART X2S.
WebEx is a network technology that allows remote control of computer systems over the internet. In the event of a problem with the SMART X2S, Bruker AXS Service personnel can remotely control, diagnose, and even repair your SMART X2S unit using WebEx.
Updating the SMART X2S Software 8.7.1 Preparing for the Software Update Power down the SMART X2S by flipping the green power switch. Figure 8.14 —Power switch Use the Administrator key to unlock the lower drawer. Figure 8.15 —Using the Administrator key Pull out the lower drawer.
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SMART X2S User Manual SMART X2S Administrator Information Some SMART X2S models have the Compact Flash card slot on the inside of the computer compartment. Look for the Compact Flash card slot on the computer compartment’ s left-hand side. Figure 8.17 —Computer compartment left-hand side (Compact Flash card slot present) If the slot is visible, proceed to Section 8.7.2.
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SMART X2S Administrator Information SMART X2S User Manual 4.3. Lift the top cover off the computer compartment, and set it aside. Figure 8.20 —Removing the top cover 4.4. Remove the 4-mm hex bolts in the top left-hand and top right-hand corners of the drawer.
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SMART X2S User Manual SMART X2S Administrator Information 4.5. Separate the drawer from the computer chassis, and set it aside. Figure 8.23 —Removing the drawer from the computer chassis 4.6. Remove the drawer panel from the computer compartment. DOC-M86-EXS127 V4...
SMART X2S Administrator Information SMART X2S User Manual 8.7.2 Replacing the Compact Flash Card Remove the Compact Flash card. 1.1. Press the small black eject button next to the card. Figure 8.24 —Ejecting the Compact Flash card 1.2. Pull the card out of the slot and set it aside.
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SMART X2S User Manual SMART X2S Administrator Information 2.2. Insert the Compact Flash card into its slot, making sure that the card orientation is the same as shown. Figure 8.27 —Inserting the Compact Flash card DOC-M86-EXS127 V4 8 - 23...
Section 8.7.1, step 4. Push in the drawer, and lock it using the Administrator key. Power on the SMART X2S by flipping the green power switch. Figure 8.28 —Power switch The instrument powers up and the computer boots. The software will automatically detect that a new card is present, perform some configuration steps, and then restart the instrument again.
SMART X2S Administrator Information SMART X2S User Manual CE Declaration of Conformity Figure 8.30 —SMART X2S CE Declaration of Conformity 8 - 26 DOC-M86-EXS127 V4...
3D view brukersupport.com Aborting Data Processing Caution notice absorption correction defined acquiring data inserting administrator retrieving SMART X2S instrument administrator using with APEX2 administrator key CD burning air-cooled design CD-R media types airflow 8-10 CE Declaration of Conformity 8-26 alerts section...
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Index SMART X2S User Manual coordination compounds generator power CPK colors crystal Greek and Roman text selection criteria size crystal information area heat dissipation help button Danger notice humidity range defined data resolution specifications Deletion of collected data 8-15 inserting your sample...
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North American service center 1-13 report display Note report summary defined reset view button opening the SMART X2S chassis safety issues optics specifications sample return after collection organic compounds scan parameters orientation matrix collection separating crystals...
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Index SMART X2S User Manual temperature temperature range zoom buttons terms and conventions Z-value thermal ellipsoid display button time displays touchscreen and styluses 8-10 interface translate buttons ultraviolet pen light Unit Cell parameters unit cell upper cover user manual structure...
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