Data Reduction and Backup

The Linux computer, ChexCSD, which houses the Cambridge Structure Database, includes the data reduction software SAINT, XPREP and SADABS. In addition the CD burner allows data collected on the diffractometer to be archived on CD-R.

If you need/want to use SMART to examine your data or redetermine a matrix, you must use the data collection computers or run the APEX II software on nulla in 32 Lewis.

If your data set appears to be normal and does not require any post-collection examination, please follow the procedures for data reduction and storage outlined below.

Actual commands to be entered are given in boldface. A word enclosed by greater than/less than symbols, e.g. <Enter> represents a key on the keyboard. If no <Enter> appears after the command, assume that you press <Enter> after typing the command. The words "dirname" and "filename" represent your filenames for the data (usually the same as the ones you used to collect the data).

TRANSFERRING DATA from the Data Collection PC

from your data directory. This will connect to ChexCSD. Login using

user: smartuse (if your data were collected on the SMART instrument)

Make sure the data have been tansferred and clean up your directory on the Data Collection PC (using the command framedel).

DATA REDUCTION

Type presaint, which will setup the defaults for data integration. Type saint with the appropriate switches for your crystal system. The command line interface for SAINT v7.07B will open. Run the integration routine (type in at the prompt).

The interface for the integration package should open. For a more specific and detailed breakdown of the commands click on this link.

The lattice type and point group of the unit cell are now entered together under the p (Point Group/Lattice type) option.

Lastly you need to set the local (y) and global (g) cell refinement parameters. You will be asked a series of questions by the program. Take the default for the first question asked (typically -1 for the local and 0 for the global refinement). For the second question answer using a number from 0, 1-9 depending on your crystal system (NOTE: 1=triclinic, 3=monoclinic, B-unique and 5=orthorhombic). And finally take the default value for the final question.

Data integration is much more rapid on ChexCSD and the data will flow past fairly rapidly. If you wish to pause the program to examine the output, press '<CTRL/S>' to halt the flow of information, and '<CTRL/Q>' to resume the integration.

Once the integration is complete, exit from SAINT and print out the merged output

Run XPREP on your data (xprep filenamem) and a new window will open. This should have in the header: XPREP Ver.2005/3 Copyright(C) Bruker-AXS 2005. Work through XPREP in the usual manner.

In addition if you choose to perform an absorption correction you will need to manually alter the threshold for direction cosines from 0.00000 to 0.005. Be careful. Note: SADABS correction is preferable and appears to give a better merging R(int) than the XPREP empirical correction.

SADABS can now be run on the data Type sadabs. You will be asked a series of questions, normally the defaults can be accepted. There is a CHEXRAY help file for XPREP and SADABS. There is also a pdf version of the Bruker manual for sadabs available here: SADABS manual.

DATA ARCHIVING

Data are to be archived on CD-R media. There is a DVD-R/CD-RW drive installed on ChexCSD. To archive your data set on CD-R (one dataset per disk) collect a blank CD-R from the spindle on the shelf near the door (and while you are at it, collect a paper sleeve for the disk). Open the DVD-R drive tray on ChexCSD and place your blank disk in the tray, close the tray. The disk goes into the drive the way up it comes off the spindle. Make sure that you are either at the ChexCSD terminal or if logged in remotely, that there are no users logged in at the ChexCSD terminal when you begin your data backup.

Change to the smartuse directory (cd /home/smartuse) or the apexuser directory (cd /home/apexuser) and type the command bakcd dirname (where dirname = the name of your sub-directory). A program will execute and you will see a few messages scroll by. This is normal. You will need to press <Enter> at the appropriate point during these messages before the burn will begin. There will be more messages including some "error messages" that are normal. The entire burning process takes about 5 minutes, so please be patient. If it doesn't take 5 minutes then there is probably something wrong. When the burn is finished the CD will be ejected. Take your CD and write the sample name (and date) on the top surface, using a soft-tipped felt pen.

You can check that your disk has been written correctly by loading it in any Windows PC or Mac. Or you can place it in any of the CD drives on the Linux boxes, open an xterm window on that computer and type the following commands:

After you type dir you should see a directory name. When you change into that directory (cd <dirname>) and perform another dir you should see a full listing of your frames.