Recently in hardware Category


SIBYLS has installed new robotics that halve the time it takes to collect a full 96-well plate, from approximately 5 hours to 2.5 hours per plate (with the potential to collect a plate in 10 minutes over the coming year). We believe this will be a game changer for many reasons. We will be able to accommodate more users per week, enable new screening methods, and have more time to offer SEC-coupled SAXS and time resolved SAXS. In addition to the new robotics, we have improved instruments for higher data quality. Our new monitor of transmitted beam intensity should greatly reduce buffer subtraction errors. We have also replaced the windows for lower background. In completing these upgrades, the stage is now set for increased sample to detector distance providing access to lower q (an upgrade that will occur sometime during the summer).

Our new pixel array detector, a Pilatus3 2M from dectris, arrived at LBNL on July 27, 2015 and was installed on the SAXS endstation at SIBYLS beamline 12.3.1. The first user data was collected on August 19, 2015.


 ADSC was very helpful in making some subtle adjustments to the detector gain maps so that the background of the images collected with our newly upgraded Q315r detector are much more uniform.

Before                                                                     After

q315r_bad_gain_2s.png q315r_good_gain_2s.png




The "Before" image is a 2 second exposure with the multilayer optics and a fully tuned beam. In addition we had some plastic cover slips in the beam to generate background scatter. The "After" image is also a 2 seconds, but with the Si(111) optics and no plastic in the beam path. We will confirm that the gain remap has fully fixed the checker syndrome, but the initial images look very promising.

The SIBYLS beamline Kohzu monochromator has often exhibited hysteresis when moving the theta 2 motor. This manifests itself in a decaying beam and suboptimal intensity. In order to fully understand the problem it helps to have a general understanding of the motors in the monochromator. The figure below illustrates the various motors and their relative motions.


The axis of the Theta motor lies on the surface of the first crystal and the angle of Theta determines the wavelength of X-rays that will be selected for a particular experiment. The second crystal is designed to take that monochromatic X-ray beam coming from the first crystal and reflect it down the beam pipe to the SAXS or MX endstation. The second crystal is ~30 meters from the crystal sample when doing a crystallography experiment and it is critical that the um-sized X-ray beam be aimed directly at the small crystalline samples. We use the Chi 2 motor on the second crystal to steer the beam from left to right (horizontal beam steering) and we use the M2 mirror to move the beam up and down (vertical beam steering).  The axis of the Theta 2 motor lies on the surface of the second crystal, and it is used to align the surface of the second crystal so that it is perfectly parallel to the first crystal thus maximizing the flux of the X-rays that exits the monochromator. Typically we tuneup the beamline before a user starts their shift and during this tuneup procedure we optimize the angle of the theta 2 motor by monitoring an ion gauge positioned at the exit tube of the mono (Imono Out) and maximize the current. If we then monitor the Imono Out gauge for several hours after the tuneup procedure is complete we sometimes see that the intensity of X-rays falls precipitously.

Imono_Out_NORMAL.png Imono_Out_BROKEN.png


Come collect data on our newly upgraded ADSC Q315r area detector.

Here is the "proof"


Our detector is gone!


It's gone! We boxed up our Q315 yesterday and sent it back to ADSC for an upgrade to the Q315r model.




Essentially this is an upgrade to the amplifiers that read out the CCDs and the other associated electronics for getting the raw images to the detector computers for processing. The fiber optic tapers and CCDs will not be replaced. The overall benefits of this upgrade are an decrease in read-out noise, an increase in speed, and the ability to use stored dark current images. Here are some excerpts from a detailed comparison performed by James Holton:

          ampgain  eo_gain    readnoise  pixel  fog photons  allowable
detector  e-/ADU   e-/photon  e-/pixel    um      /100um2   redundancy
Q315      12       7.3        27(swbin)  102.4     12.4         1.00
Q315       4       7.3        16(hwbin)  102.4      4.37        2.85
Q315R      4       7.3        11.5       102.4      2.26        5.51
M300HE     4?     11           7.7        73.2      1.71        7.29

"fog photons"/pixel is the number of extra background photons/pixel required to increase the noise in a pixel by the same amount as the read noise. Since the "fog photons" will add with redundancy, the far right column shows how many fold more images (relative to a Q315) you can spread the same total x-ray exposure over and get the same total read noise (as if you collected the data with "unit" redundancy on a Q315).  The Q315R will allow 5.5x more images than what we are doing now: 12 "fog photons"/pixel on a Q315 in swbin mode.

James goes on to compare the relative crysal sizes that will produce equivalent diffraction:

All things being equal (including the extent of radiation damage), the intensity of the spots and background are proportional to the crystal volume.  Doubling the crystal volume will double the signal (spot intensity) as well as double the background (in the ideal case of a "naked crystal" with no air scatter or other sources of background).  So doubling the crystal volume makes the noise (sqrt(signal+background)) go up by no more than sqrt(2).  Unless the crystal is bigger than the beam, or it is so thick that it attenuates the beam, radiation damage will be proportional to photons/um2, which has nothing to do with the crystal size.  This means that, for the same extent of damage, the signal/noise ratio goes as size^(3/2) if "size" is the linear dimension of the crystal.  That is, doubling the linear dimension of a "round" crystal will nearly triple the signal/noise (2.83x), and a 10% increase in the "size" (linear dimension) will increase signal/noise by 15%.

If we have some high-res spot with I/sig(I)=2 in the absence of any background or read noise, then there are (on average) 4 photons in that spot (4/sqrt(4) = 2).  Spots typically take up on the order of 25 pixels.  So, adding 0.1 "fog photon"/pixel (as on a Mar300HE) will make I/sig(I) of this spot drop from 2.0 to 4/sqrt(4+25*0.1) = 1.6.  Increasing the crystal size by 12.5% will increase the crystal volume by 42% and put 5.7 photons into this same spot (for the same exposure time and therefore the same amount of radiation damage) and bring I/sig(I) back up to 5.7/sqrt(5.7+25*0.1) = 2.0.  This means that the crystal size needed to achieve a given resolution limit on the Mar300HE is 12.5% larger than the crystal size needed to achieve the same resolution with an ideal photon-counting detector (such as the Pilatus). This is assuming there are no other sources of noise, including x-ray background.

Changing the read noise to 2 "fog photons"/pixel will make the I/sig(I) of this 5.7-photon spot drop from 2 to (5.7/sqrt(5.7+25*2)) = 0.76.  Bringing the signal up to 16.3 photons/spot will bring I/sig(I) up to 2.0 again.  This represents a ~3-fold increase in crystal volume (16.3/5.7=2.86) and a 42% increase in crystal size.  To put it another way, using the Mar300HE instead of a Q315R would let us get away with crystals 30% smaller in linear dimension for a given resolution limit (and given amount of damage).  Going from a Q315R to a Q315 (with 21 "fog photons"/pixel) will require 47.9 photons in the spot (47.9/sqrt(47.9+25*21) = 2.0) and another 43% increase 

detector    photons/spot   xtalsize
perfect          4.0     0.63 or -37%
M300HE           5.7     0.71 or -29%
Q270             7.8     0.78 or -22%
M300            12.2     0.91 or -9%
Q315R           16.3     1.00
Q315            47.9     1.43 or +43%

The take home message is that our new Q315r will be way better than that old Q315 peice of junk. We will now collect more accurate data in less time with smaller crystals.


In order to make room for the new robot sample dewar we’ve reconfigured the xyz stage and mounting hardware for the Oxford Cryojet. As you can see from these two photos the cryojet is now securely fastened to the gold sample stand.



This is the contraption that was supporting the cryojet previously:

ALS Ring Status

loading ...



Powered by Movable Type 5.2.13

March 2020

Sun Mon Tue Wed Thu Fri Sat
1 2 3 4 5 6 7
8 9 10 11 12 13 14
15 16 17 18 19 20 21
22 23 24 25 26 27 28
29 30 31