Performance of PILATUS detector technology for long-wavelength macromolecular crystallography

Performance of PILATUS detector technology for long-wavelength macromolecular crystallography

Nuclear Instruments and Methods in Physics Research A 633 (2011) S121–S124 Contents lists available at ScienceDirect Nuclear Instruments and Methods...

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Nuclear Instruments and Methods in Physics Research A 633 (2011) S121–S124

Contents lists available at ScienceDirect

Nuclear Instruments and Methods in Physics Research A journal homepage: www.elsevier.com/locate/nima

Performance of PILATUS detector technology for long-wavelength macromolecular crystallography J. Marchal , A. Wagner Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK

a r t i c l e in fo

abstract

Available online 19 June 2010

The long-wavelength MX beamline I23 currently under design at Diamond Light Source will be optimized in the X-ray energy range between 3 and 5 keV. At the moment no commercial off-the-shelf detector with high quantum efficiency and dynamic range is available to cover the large area required for diffraction experiments in this energy range. The hybrid pixel detector technology used in PILATUS detectors could overcome these limitations as the modular design could allow a large coverage in reciprocal space and high detection efficiency. Experiments were carried out on the Microfocus Spectroscopy beamline I18 at Diamond Light Source to test the performance of a 100K PILATUS module in the low-energy range from 2.3 to 3.7 keV. & 2010 Elsevier B.V. All rights reserved.

Keywords: Pixel detector Crystallography X-ray diffraction Synchrotron

1. Introduction The long-wavelength Macromolecular Crystallography (MX) beamline I23 is currently under design at Diamond Light Source. It will be dedicated for experimental phasing exploiting the weak anomalous signal of sulphur and phosphorous from native protein or DNA/RNA crystals without the need to incorporate additional anomalous scatterers and the large signals around the additional K, L and M-edges within the beamline energy range [1]. It will be ˚ but optimized in the energy range between 3 and 5 keV (2.5–4 A), ˚ I23 will also allow the use of X-ray energies up to 12 keV ð  1 AÞ. detector requirements are:

 high DQE between 3 and 12 keV and especially in the 3–5 keV  

range, operation under HV or in helium environment (preferably HV), large angular coverage ð2y ¼ 7903 Þ, ideally spherical, cylindrical or several hinged flat detectors.

At the moment no commercial off-the-shelf detector with high quantum efficiency and dynamic range is available to cover the large area required for diffraction experiments in this energy range. The pixel detector technology used in the PILATUS detectors could overcome these limitations as the modular design could allow a large coverage in reciprocal space and high detection efficiency. PILATUS detectors are hybrid pixel detectors which have been developed for MX at the Swiss Light Source (SLS)  Corresponding author. Tel.: + 44 1235778919; fax: + 44 1235778783.

E-mail address: [email protected] (J. Marchal). 0168-9002/$ - see front matter & 2010 Elsevier B.V. All rights reserved. doi:10.1016/j.nima.2010.06.142

[2]. Single module (P100K) and multi-module PILATUS detectors (P300K, P2M, P6M) commercialized by DECTRIS [3] are installed on several X-ray diffraction beamlines at Diamond Light Source [4]. The specifications of PILATUS detectors can be found in Refs. [5,6]. In this study we investigate the feasibility of trimming the energy threshold of pixels with low-energy X-rays (2.3–3.7 keV) and the effect of several charge sensitive amplifier (CSA) gains on ‘‘minimum trimmable energy’’. The analogue pulse width associated with each CSA gain setting was measured. Finally, flood-field images and powder diffraction images where acquired with low-energy X-rays.

2. Experimental set-up A PILATUS P100K detector was tested on the spectroscopy beamline I18 at Diamond Light Source. In order to trim the detector pixel thresholds, X-ray fluorescence from different powder samples was used as source of monochromatic X-rays. The X-ray fluorescence characteristics of the sample materials used in this study are summarized in Table 1. To minimize elastic scattering the detector was placed perpendicular to the incident X-ray beam at a distance of 100 mm between sample and detector window. The energy spectral distribution was measured with the I18 4-element Vortex silicon drift detector mounted at 451 to the incoming X-ray beam to distinguish the different contributing factors like elastic scattering, sample and other sources of X-ray fluorescence. To minimize X-ray attenuation, detector and sample were placed in a helium-filled plastic bag as shown in Fig. 1. The same set-up

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Table 1 Samples used for detector threshold trimming. Sample material

Beam energy (keV)

K-edge (keV)

Ka energy (keV)

KBr NaCl S8 CaCO3

3.650 2.850 2.500 4.070

3.608 2.822 2.472 4.039

3.314 2.622 2.308 3.692

Fig. 2. Energy threshold calibration (VCMP vs. X-ray energy). DECTRIS had supplied detector energy calibration and trimfiles for this detector for mid-gain (VRF ¼  0.2 V) and low-gain (VRF ¼  0.3 V) settings. Additional calibration data were obtained during our experiment for VRF ¼  0.15,  0.10 and  0.05 V.

Fig. 1. Photograph of the test set-up on I18, showing the PILATUS P100K detector and powder pellet positioned in a helium-filled bag on the synchrotron beamline.

was used to acquire flood-field images. However, detector to sample distance was reduced to 30 cm from the sample in order to produce a more uniform illumination.

3. Results 3.1. Threshold trimming The overall energy resolution of a PILATUS detector can be improved by trimming the voltage thresholds of the comparator in each pixel [6]. Threshold trimming is performed by means of a 6-bit DAC in each pixel which offsets a global threshold value (VCMP). The first step of a trimming procedure consists in scanning the comparator threshold voltage (VCMP) without applying any trimbit correction. This produces the S-curves of mean count rate as a function of comparator threshold. The VCMP-energy calibration shown in Fig. 2 was obtained by plotting the VCMP value corresponding to the inflection point of the S-curve as a function of the energy of the monochromatic X-rays used to generate the S-curve. Energy threshold calibration was performed for several values of the detector CSA gain. The gain and shaping time of the CSA can be varied using the DAC voltage VRF between 0.03 and 0.6 V [6]. For X-ray energies between 5 and 20 keV VRF is set to the mid-gain value of  0.20 V leading to a small detector deadtime of 200 ns. With low energy X-rays, higher gain settings are required to discriminate counts from the background electronic noise, at the expense of detector dead-time which increases at high gain settings. Accurate threshold trimming of the module can be achieved at a given X-ray energy and CSA gain setting (VRF) only if the S-curve reaches a plateau (not completely flat due to charge-sharing) before getting into electronic noise. S-curves for three CSA high gain settings and several X-ray energies are shown in Fig. 3 after conversion of the VCMP scale into energy. S-curves reaching a

plateau could be obtained for X-ray energies down to 3.3, 2.6 and 2.3 keV for VRF values of  0.15, 0.10 and  0.05 V, respectively. The threshold trimming routine performs threshold scans for each trimbit value [0–63] and computes the trimbit correction required for each pixel in order to reduce threshold dispersion. Distributions of trimbits centred around trimbit value 32 and decreasing to 0 on each side of the trimming range were obtained for X-ray energies of 3.7, 3.3 and 2.6 keV at each of the three different gain settings of VRF ¼  0.15, 0.10 and  0.05 V. This shows that when using a detector threshold trimmed at 2.6 keV, a gain setting of  0.15 V can be used, corresponding to a short detector dead-time of 300 ns. For 2.3 keV the following problems occurred:

 VRF ¼ 0.15: software crash during the scan,  VRF ¼ 0.10: produces a trimbit distribution with an unusual shape shifted to the low trimbit values,

 VRF ¼ 0.05: produces a trimbit distribution of normal shape slightly shifted to high trimbit values but with two bumps at trimbits 4 and 12 corresponding to some pixels (10% of active area) located at the chip boundaries. 3.2. Flood-field The detector was placed at 30 cm from the CaCO3 powder sample at an angle of 901 with the beam. X-ray fluorescence of E¼3.692 keV was used to produce flood-field illumination. Flood field images were acquired with the comparator threshold and trimbit correction data generated for 2.6 keV X-rays and a CSA gain setting of VRF ¼  0.10 V. On the raw flood-field image, noisy pixels are present close to the edges of the 16 chips composing the detector modules. These noisy pixels represent  3% of the detector active area and correspond to pixels which have not been correctly trimmed during the threshold trimming procedure. A flood-field correction is required to remove these remaining pixel-to-pixel variations. Flood field correction coefficients were obtained from the sum of 10 flood field images. The validity of flood-field correction for this energy/trimbit combination was tested by comparing image noise in a raw image with noise in a flood-field corrected image. The variance calculated over a region of interest of 50 by 50 pixels in the flood-field corrected image is 1.47  104, very close to the mean intensity 1.34  104 calculated

J. Marchal, A. Wagner / Nuclear Instruments and Methods in Physics Research A 633 (2011) S121–S124

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Fig. 4. Powder diffraction at 4.070 keV from a NaCl powder sample with an energy threshold of 2.6 keV (a) and 3.3 keV (b). Pixel thresholds were equalized using trimming data obtained with 2.6 keV X-rays. A CSA gain VRF setting of  0.10 V was used. The bottom picture (c) shows the intensity in the pixels along row 150 of the module for the two different thresholds.

3.3. Powder diffraction Powder diffraction patterns from a NaCl sample were taken at an X-ray energy of 4.070 keV. Two different threshold settings of 2.6 and 3.3 keV at a CSA gain setting of VRF ¼  0.10 V were chosen to see the effect of suppression of fluorescence from Cl at 2.622 keV. Fig. 4 shows that for the higher energy threshold the background could be significantly reduced.

3.4. Detector dead-time Fig. 3. Plot of mean counts per pixel as a function of threshold energy obtained during the threshold trimming procedure by scanning VCMP for VRF ¼  0.05,  0.10 and  0.15 V with four powder samples. (a) VRF ¼  0.05 V; (b) VRF ¼  0.10 V; (c) VRF ¼  0.15 V.

over the same region of interest. This demonstrates that floodfield correction effectively reduces image noise which gets closer to the Poisson noise limit.

The detector dead-time as a function of CSA gain was approximated by measuring the width of analogue pulses at the output of the preamplifier and shaper circuit of a pixel. X-rays of 2.6 keV were incident on the detector and pulse width (rising time+ time to return to baseline) was measured on a digital scope. Results summarized in Table 2 are in agreement with the deadtime measured by DECTRIS by fitting data to a paralysable counter model for standard CSA VRF settings [5].

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Table 2 Width of analogue pulses generated by 2.6 keV X-rays as a function of CSA gain (VRF) setting. VRF (V)

Pulse width (ns)

 0.05  0.10  0.15 (high gain)  0.20 (standard)  0.30 (low gain)

 4000  800  300  200  100

These presented results are very encouraging and suggest that PILATUS technology can be suitable for long-wavelength MX. Further tests will be needed to refine the trimming procedures and investigate performance variations from module to module. The efficiency of standard PILATUS technology for X-rays below 3 keV is limited by the attenuation of the 1 mm Al and 122 mm doped silicon layer on the front of the sensors (  60% transmission at 3 keV). The performance of sensors with thinner Al layer should be investigated as well as the feasibility of operating the sensors in vacuum.

4. Conclusion Acknowledgements It was possible to trim the PILATUS 100K module at an energy of 2.6 keV for a CSA gain setting of VRF ¼ 0.15 and  0.10 V corresponding to an analogue pulse width of 300 and 800 ns respectively. With the latter setting, pixel-to-pixel nonuniformities remaining after trimming could be removed by flat-field correction. NaCl powder diffraction images with different energy thresholds showed significant reduction of the X-ray background after adjusting the threshold above the Cl X-ray fluorescence (2.6 keV). Trimming at 2.3 keV was not conclusive. It was feasible for most of the pixels ð  90%Þ for a CSA gain setting VRF ¼  0.05 V corresponding to a pulse width of 4 ms. Chip instabilities were encountered with this gain setting, which could not be fully understood during the limited time of the beamline experiment.

The authors are grateful to I18 beamline scientists Fred Mosselmans and Paul Quinn who provided beamtime and support during detector test experiments. Technical advice from DECTRIS on the use of PILATUS threshold trimming routines was also greatly appreciated. References [1] [2] [3] [4] [5] [6]

K.D. Carugo, et al., J. Sync. Rad. 12 (2005) 410. G. Huelsen, et al., J. Appl. Cryst. (2006) 550. DECTRIS Ltd. website: /http://www.dectris.comS. J. Marchal, et al., Nucl. Instr. and Meth. A 604 (2009) 123. P. Kraft, et al., J. Sync. Rad. 16 (2009) 368. P. Kraft, et al., IEEE Trans. Nucl. Sci. NS-56 (2009) 758.