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Lesson 16. CCD Detectors Visit the Lab. Charged Coupled Device. The ccd is essentially a digital camera To keep noise down it is cooled It is almost realtime. Does not have as low a noise level as image plate but is much better than scintillation detector.

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lesson 16
Lesson 16
  • CCD Detectors
  • Visit the Lab
charged coupled device
Charged Coupled Device
  • The ccd is essentially a digital camera
  • To keep noise down it is cooled
  • It is almost realtime.
  • Does not have as low a noise level as image plate but is much better than scintillation detector.
  • Does not detect x-rays but light emitted by a phosphor.
newer developments
Newer Developments
  • Very large CCD chips that do not need taper.
  • These are 16 Mega pixel chips.
  • Much more sensitive which improves signal to noise (over 200 electrons/photon)‏
  • Read out is faster.
the x ray lab
The X-ray Lab
  • FR571 Rotating Anode Generator producing a 0.1X1.0 mm beam.
  • A Nonius KappaCCD Diffractometer
  • Software:
    • Nonius Collect Package
    • EvalCCD
    • Denzo
some kappaccd basics
Some KappaCCD Basics
  • The computer that runs the ccd is called the server. It runs Windows98 and the monitor and keyboard are on the rotating anode.
  • It can perform basic operations and is used in aligning the crystal in the beam and checking crystal quality.
  • To keep other users out there is the concept of MASTERSHIP. When the server has MASTERSHIP no other computer can operate the ccd.
client computers
Client Computers
  • These are LINUX computers that connect to the server over the internet. (Note LINUX is case sensitive).
  • They run programs that do higher level calculations and then instruct the server to carry them out.
  • Contain the Nonius software COLLECT package
indexing
INDEXING
  • There are two approaches to indexing crystals
  • One is DENZO a standard package used for macromolecular crystals.
  • The other is DIRAX or CELL_NOW
  • They require different input frames.
indexing with denzo
INDEXING WITH DENZO
  • Need to collect 10 frames each of 1° rotation.
  • DENZO then indexes the frames.
  • It uses partial spots—spots that appear on more than one frame.
  • Can be run automatically or under user control
  • Very robust
  • Cannot index twined crystals—produces only one orientation matrix
  • Denzo is started with the command kc.
dirax cell now
dirax --cell_now
  • These need the pixel location on the frame and also the rotation angle value which cannot be directly determined.
  • Collect on 5° frame.
  • Then collect the same frame while moving chi by 10° while doing the other rotation. The change in the location of the spot between the two frames can be used to determine the rotation angle
  • Collect 4 sets of these pairs of frames.
dirax
DIRAX
  • Requires more user interaction.
  • Can index twins or determine multiple orientation matrices.
  • Should always be run even if cell_now.
  • Called by the command “ndirax gui”
cellnow
cellnow
  • Cellnow is a local program that runs cell_now and creates the proper orientation matrices.
  • Cell_now is a George Sheldrick program
  • Very automatic but uses a good deal of time
  • Can determine multiple orientation matrices but only if one unit cell is present (one compound).
  • Sometimes obtains cells that are a multiple of that found in dirax. These are incorrect.
supergui
supergui
  • This is the program that guides you through the entire indexing, data collect, and integration process.
  • You use it by pushing buttons.
  • It is fairly foolproof.
  • Supergui in the Purdue lab also posts the structure name on the monitor on top of the rotating anode. To not post the name use superguinl.