From: John Philo <jphilo@mailway.com>
  To  : Rasmb <rasmb@alpha.bbri.org>
  Date: Mon, 13 Aug 2001 11:05:22 -0700

RE: optical alignment and image contrast (was: wiggles in dc/dt plots)

In addition to the issues that Tom Laue and others have discussed, my
understanding is that the magnitude of these 'wiggles' is influenced fairly
significantly by the alignment of the interference optics, and possibly also
by the contrast/brightness settings.

I was told by Jerry Porter at Beckman more than a year ago that he had
developed a better alignment procedure that reduces the fringe 'jitter',
'wagging', and speed-dependent noise, and presumably that alignment is now
used on the new machines. I doubt though that older machines have ever been
re-aligned. I don't know if Jerry is yet back from medical leave but if so
perhaps he will comment.

I believe I've heard that Dave Yphantis, the UConn center, and perhaps Walt
Stafford also, use a different optical alignment procedure. If that is true,
perhaps they could comment in this forum on why they use an alternate
alignment and what that accomplishes, and then perhaps post details on their
procedures on the NAUF web site or the RASMB web site?

I also recall hearing that the magnitude of the phase errors discussed by
Tom and Art Rowe depends on the contrast and brightness settings for the
fringe images, with some people believing strongly that the default settings
are definitely not the right settings. Again, if this is true then I would
encourage people to comment briefly here and then post some examples of
'correct' fringe images on a web site so everyone can see what is 'correct'.

John Philo
Alliance Protein Laboratories
www.ap-lab.com

-----Original Message-----
From: Tom Laue [tom.laue@unh.edu]">mailto:tom.laue@unh.edu]
Sent: Monday, August 06, 2001 6:38 AM
To: Neil Errington; Gunther.Kern@astrazeneca.com; rasmb@alpha.bbri.org
Subject: RE: wiggles in dc/dt plots


Hi Folks,
The wiggles referred to can come from a couple of sources.
1- Jitter in timing the laser pulse: there was a firmware problem in setting
up the timing of the laser pulse. The software loop to do this required ~1.5
milliseconds, which is longer than the period of rotation at high rotor
speeds, and caused problems in data collected at rotor speeds above ~55,000
rpm. There was a firmware fix released about 18 months ago that fixed this
problem. Be sure you have the most recent version of the EPROMs in the XLI.
2- There is an outstanding issue with the heaters and baseplate flexing that
David Yphantis and Jeff Lary have documented. This problem is likely due to
the mounting of this lens to the baseplate... a problem stemming from my
design. The problem was reported to BCI four years ago, and I have been told
that BCI has a possible fix. To my knowledge the fix hasn't seen the light
of day. A related problem is caused by thermal gradients across this lens,
resulting in a 'twisting' of the fringe image. The fix from BCI should help
this problem, too. The magnitude of these fluctuations is about 0.01-0.1
fringe, far worse than the intrinsic capabilities of the design (~0.0006
fringe).
3- The Fourier analysis of the fringe patter can result in oscillations in
the reduced data. The cause is a mismatch in the frequency of analysis and
the spatial frequency of the fringes, and it leads to a periodic oscillation
in concentration calculation. Typically, the magnitude of this oscillation
is 0.003 fringe or so, though it can be worse if the image is not good (i.e.
there is dust on the camera). This problem can be minimized by calibration
of the pixels per fringe (available under the detail settings for the
interference optics). An even better fix is to replace the camera with one
containing more pixels in the vertical direction, though this adds a
one-time cost of about $12,000. David Yphantis has shown that with a larger
array, and elimination of the temperature fluctuations will result in at
least a ~100-fold  improved precision. Are you interested in having the
improvements available?
Best wishes,
Tom

University of New Hampshire
Rudman 379
46 College Rd.
Durham, NH 03824-3544
Phone: 603-862-2459
Fax: 603-862-0013