Quick Start Urs Guide for
Bruker SMART APEX II Diffractometer
ROUTINE DATA COLLECTION
Software version APEX2 v2.1-0
J. Tanski 2/15/06, rev. S. MacMillan 1/14/07
This guide is uful for routine data entry, collection and reduction.
The APEX2 v.2 Ur Manual contains more information and instructions. Plea e JMT for instructions on how to start the X-ray generator and
cryostream.
1.0There are two X-ray log books: a composition book for note taking and
a binder that contains pertinent information and finished structure
tables. Both notebooks should be kept up-to-date. Before starting a new data collection, begin a new page (odd pages only) in the composition log book.Each entry should ultimately contain the date, names of urs (including students and non-Vassar urs), sample filename, temperature, crystal size and description of the crystal.
The format of the sample filename is the first and last initial of the rearcher, the log book page number, and one element symbol that describes the compound. For example, if J oe T anski wants to collect data on a V anadium compound and writes information on page 373 of the log book, then the sample filename will be JT373V.
关于法律的知识
The binder log book contains two forms that should be filled out as more information is obtained. The goal of the notebooks is to streamline the massive amount of information that flows into and around the X-ray facility. Plea help us stay organized!
Note: If the Apex2 window is already open, skip to Step 1.2iii
棒球英语怎么读1.1To begin, double click the BIS icon at the top of the desktop screen.
BIS is the program that links the hardware and the APEX2 software ud for t-up, collection and reduction. A dialogue box will appear;
confirm that the distance is t to 5.483 cm and click OK.主甲板
Information, including the distance (5.525 cm), detector temperature
(~ -60°C) and generator status (20 kV, 5 mA), will appear in the BIS window.
1.2Double click the APEX2 icon. Select I NSTRUMENT-C ONNECTION.
健力宝广告The host name appears by default (Bruker3b-rver); click C ONNECT.
It will take about 15 conds to establish the connection.
i.To open an existing project, lect S AMPLE-O PEN. A list of projects驾照考题
will appear. Find the desired project, highlight it, and click OK.
ii.To create a new project, lect S AMPLE-N EW. A dialogue box will appear with three fields (name, group and folder).
First, create a new folder:
Folder: The default for this field is C:/frames/guest. U the folder
icon to brow to C:/frames/guest/APEXUrs/VassarUrs/Ur.*
Create a new directory within the appropriate ur folder using the
new folder icon () and name the folder as the sample filename.
Hit ENTER to create the folder (you must hit enter!), lect the folder,
and then click OK.
*Note: Ur is the actual name of the rearcher (i.e. Tanski). If
data is being collected for a non-Vassar ur, brow to
C:/frames/guest/NonVassarUrs/Ur instead of the path given
above.
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Name: U the sample filename given in the X-ray log book (i.e.
JT373V).
Group: The default is “Urs”; there is no need to change this field. The left side of the APEX2 window has a task bar with Setup, Evaluate, Collect, Integrate, Scale, Examine Data, Solve Structure, Refine Structure, Report and Instrument buttons. U the buttons to navigate the program through the various stages of the experiment.
1.3Select C ENTER C RYSTAL. The video microscope screen will open. If
the goiniometer is not zeroed and the crystal has not yet been mounted, click M OUNT (lower right corner of the APEX2 screen) and place the crystal on the goiniometer. Click R IGHT to drive the goiniometer to the right position; manually adjust the loop such that the edge of the loop is perpendicular to the plane of the video microscope screen. This will make centering the crystal easier.
See p. 5-6 in the Apex2 Ur Manual for instructions on how to center the crystal.
大风灾害The crystal should not extend past two and a half rings on the crosshairs. The ÅÆ button can be ud to measure the crystal (100 μm = 0.1 mm). Record the crystal size in the log book.
When the crystal is centered, lower the video microscope window and click the “X” button (be sure n
ot to click the APEX2 “X” above it, as this will exit the entire program) to clo the centering window.
1.4Select S ETUP-D ESCRIBE. Enter the molecular formula (with no
spaces), the primary crystal color (if the crystal has no color, it is colourless, not n/a), dimension, and shape (i.e. block, plate, needle, bulk) in the appropriate fields. To write the information to the databa, clo the window by clicking the “X” button (not the APEX2 “X” above it).
1.5Select E VALUATE-D ETERMINE U NIT C ELL. Click R UN (right side of
APEX2 screen) to accept the default matrix collection time (5 conds).
It takes about 12 minutes to collect the matrix frames, harvest the spots and index the cell. There should be green check marks in each box as the indexing steps are completed. Record the unit cell in the log book.
Click C LOSE when all the steps are done.
If the cell is acceptable, skip to Step 1.7
If the cell is not acceptable, it is possible to either manually determine the unit cell or to work further with the cell (suggested for weak or poor data, or for a suspicious unit cell).
i.Manually determine the unit cell.
a)To obtain a new unit cell from matrix runs only, delete the unit cell
and reflections by clicking the D ELETE buttons. Click H ARVEST
S POTS and brow to find the first image of the matrix collection
(matrix_01_0001.sfrm). Select the number of runs and images to
u (3 and 20, respectively). It is best to be have an I/σ of ~10 on
the More/Fewer Spots scroll bar.1 Click H ARVEST at the bottom
right of the screen.
Click I NDEX, move the More Spots scroll bar towards “More
Spots” (I/σ ~10). Click I NDEX at the bottom right of the screen.
If a reasonable unit cell is obtained, lect it and click A CCEPT.
Continue with the instructions in Part ii below.
b)To read in additional reflections from data frames, click on
H ARVEST S POTS and brow to find the first image of the data
collection (samplefilename_01_0001.sfrm) and t the number of
runs (1) and number of images to u (50-100). It is best to be
have an I/σ of ~10 on the More/Fewer Spots scroll bar. Click
H ARVEST at the bottom right of the screen.
Continue with the instructions in Part ii below.
ii.Working further with the unit cell.
a)Move the More/Fewer reflections scroll bar towards “More
Reflections” and click R EFINE. Move the scroll bar stepwi
towards “Fewer Reflections”, refining once or twice each step,
until the unit cell parameters have refined to at least 2 decimal
places and the detector translation distance is minimized. It is also
advisable to alternate refinement parameters with the D ETECTOR
T RANSLATION and B EAM C ENTER boxes checked OR with the
D ETECTOR O RIENTATION box checked. Stop moving the
More/Fewer reflections scroll bar to the right when a large portion
of the reflections refined are removed from the refinement. The
出出国spots on the frames should be predicted (covered by the blue
circles). Click A CCEPT.
1 Adjusting the I/σ for harvesting spots and unit cell determination will often be necessary. For weak data, decrea I/σ; for very strong or twinned data, increa I/σ.
b)Click B RAVAIS and lect the appropriate lattice. After clicking
A CCEPT, click R EFINE and move the More/Fewer Reflections
scroll bar towards “More Reflections”. Continue to refine the cell
as described above.
c)Accept the unit cell and record it in the log book. If the detector
translation distance did not refine to near zero, more reflections
will have to be read in from data frames and the unit cell refined
further (Part i.b). If this must be done more than once, be sure to
change the number of the first data frame to one more than the last
frame read in the previous time.
Click the “X” to clo this window.
Note: Data collection may be started even if there is no unit cell; it
is possible to harvest spots from the data frames later to determine
the cell.
1.6Skip this step unless necessary. Select C OLLECT-O RIENTED S CANS.
Repeat the following procedure for each vector a, b, and c. Note that all of the scans may not be possible on our fixed chi platform.
Click on a vector, then C ALCULATE, then G O T HERE. After the goiniometer drives to the correct position, click M AKE S CAN.
Record the appearance of the axial photographs in the log book. For example, mirror symmetry will be obrved for the b-axis of a monoclinic cell. Click the “X” to clo this window.
1.7Select C OLLECT-E XPERIMENT. To collect a standard hemisphere, skip
to Step 1.8 (advid).
To prepare a unique data collection strategy, lect D ATA C OLLECTION S TRATEGY. Make sure the distance is 55.25 mm and the resolution is <
0.75 Å. The program must “Scan” after changes are made. Set the first
exposure time to 10 conds (30 for weakly diffracting crystals), hit ENTER, and click S AME.
Under “Strategy”, lect the length of data collection desired. 12 hours is a good place to start; the length of time will depend on the crystal quality and unit cell symmetry.
