Is the Beam Center Correct?
We have had a couple of instances when the beam center was incorrect in the header of our images. The header of an image is written out when you collect a diffraction image. The header may contain the wavelength, collection time, beam center and oscillation step size, which are read by data processing software (in this case Ipmosflm).
Unfortunately, the information contained within the header may not be correct.
How can you look for to tell if your beam center is incorrect?
One way is by looking at where the Bragg reflections are predicted vs. where they actually are located. It is important to check if the orientation of the lunes and the spacing between Bragg reflections looks reasonable. If they are not then you may an issue with your unit cell and/or space group and not a beam center problem.
If you are having trouble seeing the offset in the video here is a screen shot:
The blue arrow is pointing toward the Bragg reflections while the red arrow indicates the predicted reflection locations. Also you can see that there are fewer Bragg reflections (dark spots) than what is predicted (yellow squares) which is a sign that there is a problem.
chempilot
February 11th, 2010 at 2:43 PM #
great! i’ll stay tuned to see how to fix it….
Oliver Clarke
February 11th, 2010 at 11:24 PM #
If you have ice rings, use the “fit beam centre to circle” function in mosflm (ipmosflm, at least – not sure about the new one) to get a very precise estimate of the beam centre.
Labelit.index is also excellent for getting an initial estimate of the beam centre given good diffraction – the autoindexing algorithm it uses appears very robust.
Sean
February 12th, 2010 at 11:52 AM #
@chempilot coming
Oliver you are stealing my glory – just kidding thanks for the helping.
Artem
February 12th, 2010 at 9:16 PM #
1. on many beam lines the weight of the detector can significantly distort the support on which the detector rests – therefore beam center (absolute Y and even sometimes X if there’s a twist component) may be a function of distance (this is not supposed to happen, especially with A-frame set up – but it does). If this happens to you – be aware of beamline geometry and adjust according to the direction of world axes within your system.
2. beware of misindexing by 1 – in some crystal systems, particularly with large axis in a special position indexing cannot properly discriminate between n and n+1 order reflections – this results in ‘indexing’ but obviously during integration and scaling things go south very quickly. This is commonly associated with beam center definition as well.
3. Beam line staff is a good source of ‘fresh’ beam center information. In fact on most beam lines it’s their duty to determine and propagate correct beam center (and other variable positional information as needed) – and if things aren’t what they should be please do mention this to your user support person as they likely very much want to know so the issue may be fixed. By doing so you will also be doing a favor to the users coming on after you.