Commented Master Tender Document D8 questeco

The detector shouldn’t be prone the signal-blurring effect (blooming) seen for high intense reflections with some detector technologies and the sensor must therefore have intrinsic anti-blooming capability as verified by the manufacturer of the sensor. A detector which can be operated in a shutterless data collection mode,maximizing data quality while minimizing shutter jitter will be preferred.

A rate meter routine to automatically sum up and display pixels in center of detector for alignment shall be provided.

CMOS Detectors Unique Performance Benefits of the PHOTON 100 CMOS Active Pixel Sensor

Due to its unique design embedding a scintillator optimized for home laboratory wavelengths the PHOTON 50 detector is the only CMOS detector offered on the market with high sensitivity usable for both: soft radiation, such as Cu, and hard radiation, such as Mo and Ag. The Dectris Pilatus detector was designed for synchrotrons to satisfy structural biology demands and is optimized for energies < 8 keV. In CCDs coupled to tapers offered by other suppliers, demagnification leads to a loss of up to 80% of the signal and introduces spatial distortion and blurring from the glass fibers (which are slightly twisted in the glass pulling process). The CMOS sensor used in the PHOTON 50 is twotimes larger than the conventional Kodak 2K CCD chip used by other vendors. Lacking a fiber optical taper minimizes distortion leading to more accurate positional data information and hence more accurate unit cell parameters and bonding geometry. Bruker is offering a 3-year warranty for the PHOTON 50.

Đàu đò Atlas CCD của Agilent lớn hơn PHOTON 50 liên quan tới kích thước và khu vực hoạt động. Tuy nhiên, is requires a 1:2 reduction taper, losing 80% of the reflection intensity in the taper. The rarely sold EOS detector can’t compete. The taper ration of 1:1.3 results in a loss of 63% “only”.

Rigaku has given up on CCDs and almost exclusively offers Dectris’ Pilatus 200 third party detector with a 5% blind area. This detector is offered as “noise-free”, which it is not. This can be seen in a flood field experiement with a relatively low count rate. Additonally, the Pilatus 200 suffers from dead-time effects for high count rates and a signal loss due to blind areas within each pixel. The design of the Pilatus 200 is 10 years old. Dectris is already working on a replacement system.

11. Detector mount

The Atlas has to be operated at a larger DX sample to detector distance; 55 mm is the minimum DX on the Agilent goniometer we have seen. Recent tender replies indicate 35 mm as well.

With curved image plates offered by Rigaku, there is no possibility to move DX at all – the radius of curvature is fixed. Thus, rejection of systems without a movable detector will lock-out the RAPID II Imaging plate system.

12. Integrated Microscope

13. Small accessories

14. Quality - General

Unit cell constants must satisfy the equation:

standard deviation of a/ length of a < 0.0003

After structure solution and refinement the R figure of merit must be less than 3.0% for Mo and less than 4.5% for Cu. The goodness of fit must be less than 1.50. AC

15. SOFTWARE

Remove Linux or Windows 7 option respectively, whenever appropriate. We’d prefer to reduce the number of Linux systems to a minimum.

Agilent can’t offer Linux support.

Rigaku can’t offer Linux support.

The software shall allow remote access to the instrument including diffractometer, goniometer and X-ray generator functions to setup the experiment, view data as collected, process the data and solve and refine the structures remotely or off-line. Preferably, the use of third party remote desktop software for the remote connection should be avoided. USP

Note:

APEX2 connects via a TCP/IP to BIS running on the instrument’s controller PC.

Agilent can only provide access to the instrument’s PC via remote desktop software.

Rigaku can only provide access to the instrument’s PC via remote desktop software.

The measurement software shall have a graphical instrument representation for real-time display of the current instrument configuration based on component recognition, real-time validation, conflict detection, and path planning. USP.

While the system is under warranty software updates should be made available for download to users free of charge three to four times per year.

The software provided shall be able to diagnose twinned and split crystals and to index twins by visual separation of the reciprocal lattice components and by automated indexing using full and difference vector algorithms. The software shall be able to handle the reflection array as two or more subsets with separate orientation matrix for each component in order to compare the set of matrices and to determine the twinning law or the non-crystallographic rotation in split crystals. The software provided shall conveniently support all further data acquisition and data processing, data scaling steps, including a proper absorption correction. Tenderers are encouraged to provide examples for properly absorption corrected multi domain samples and state how many domains the package can handle at a time. USP

Note:

Throughout the entire package APEX2 supports eight domains.

Agilent can only work with 4 twins at a time (according to www.x-rayman.co.uk by pmueller » 13 Jul 2010). 6 domains are not unusual. So, one can’t use CrysAlis for data-indexing and integration of these 6 twin components.

Rigaku’s TwinSolve can only handle 2 domains only.

Application Note SCD 375 Pseudo Merohedral Twinning: How to Treat a Six-fold Twin, DOC-A86-EXS002

The system shall include two proven absorption correction routines: one for numerical face indexing, and the second employing semi-empirical methods using direction cosines. It should be possible to combine both routines in particular for very highly absorbing compounds. The software shall apply an incident beam correction and a diffracted beam correction for reflections on the same frame. The software shall incorporate algorithms routines (e.g. those from Blessing) to give statistically correct sigma values for each reflection; automatically apply corrections such as for detector geometry, crystal orientation particularly in capillaries, and crystal decay. The software shall check for internal consistency based on the Laue class and shall be able to properly down weight outliers.

The data collection segment shall provide the following features at minimum:

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  Crystal screening via initial one minute rotation frame and consecutive tools for frame analysis such as: display of 3D reflection profiles, rocking curves, zoom up to pixel level, circle cursor for determination of the resolution, display of background counts and integrated intensities on reflection level.
  
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  Automatic collection of multiple frames suitable to determine unit cell in narrow frame mode which provides the best centroids of reflections and hence the best unit cell parameters, or selection of wide frame indexing followed by unit cell refinement after data collection.
  
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  Fast and reliable automated unit cell determination using phi, omega or phi/chi scans based on auto-indexing routines featuring full vector and difference vector algorithms. Furthermore, the selection of conventional reduced primitive cell and assignment of indices to reflections, including ability to handle twinned crystals is required.
  
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  Automatic calculation of least-squares orientation matrix and unit cell parameters, with nonlinear least-squares fit to account for errors in the crystal centering.
  
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  Automatic Bravais lattice determination to display possible higher symmetry unit cells and select best choice.
  
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  Ability to take oriented photographs about specified direct or reciprocal axes, exploiting the full kappa goniostat capability, and with selectable overlay of predicted reflection positions.
  
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  Ability to collect, integrate and merge data with detector at multiple settings of 2theta (on-axis and off-axis, 2theta-swing).
  
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  Automatically repeated collection of frames possessing very strong reflections applying either shorter exposure time per frame or inserting a proper absorber material.
  
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  Automated corrections for spatial and intensity calibrations.
  
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  Calculation of unit cell parameters based on all available reflections after data collection, if desired.
  
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  Contain a reciprocal space display for examination and manipulation of reflection arrays, which allows removing spurious reflection for better indexing; detection of twinning and separation of twin domains for subsequent indexing; Automated and interactive determination of modulation q-vectors from commensurate or incommensurate samples and subsequent data integration and scaling.
  
• 
  Facilitate the determination of rotation angles or twin laws between domains by comparing unit cells
  

The data integration software shall use a 3D-algorithm and be able to operate as a background task to process each frame as received from the instrument. For optimum signal-to-background and best unit cell parameters narrow frames capability, slicing each reflection in 5 to 7 frames using a frame width as small as 0.1 degree rotation per frame to get best reflection centroid information is essential, while for a maximize data collection efficiency the capability to collect and integrate data in wide frame mode with a several degrees rotation per frame is important. The package offered should be able to handle both types of data sets on the same high quality level.

The output shall include scaling, output of statistics, merged or unmerged reduced data, and calculation of direction cosines for absorption correction.

Pseudo Precession images shall be generated from data collection frames, to enable detection and investigation of twinning, superstructures, modulated structures, and diffuse scattering.

The software for data scaling and absorption correction shall be based on the intensities of symmetry-related reflections measured at different angular settings. Overlapping reflections from multiple-domain samples shall not be rejected but properly processed and kept in the data set. Processing of modulated structure data ready for further processing (e.g. in JANA) shall be possible. The system shall include output data files directly compatible for input to SHELX software, including direction cosines for reflection data.

The structure solution and refinement software, such as SHELXTL, provided shall include the following features:

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  Valid for all space groups in all orientations with automatic space group determination.
  
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  Instructions in simple free format.
  
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  Ability to display weighted and color-coded reciprocal lattices, similar to Precession photographs, and to display contoured Patterson sections.
  
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  Direct methods with negative quartets, phase annealing from random starting sets, partial structure recycling and interpretation of pseudo symmetric and twinned structures.
  
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  Full matrix least-squares refinement for up to 1200 full matrix parameters, and blocked or conjugate gradient refinement up to 5000 atoms. Minimization to be based on F²-refinement, with output of crystallographic R factors for F and F².
  
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  Least squares refinement to include refinement of merohedral and other twins, rigid groups, isotropic extinction and powder diffraction data, geometric positioning and constrained refinement of hydrogen atoms, and disordered groups refined with restrains; automatic constraints for atoms in special positions constraints and restraints to be applied from known structures.
  
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  Automatic interpretation of heavy atom Patterson maps and computer-aided interpretation of pseudo symmetric structures and twinned structures, plus rotation/translation search for oriented fragments or single atoms based on combined Patterson search and direct methods and packing.
  
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  Ability to display and plot molecules, up to 10,000 simultaneously, with thermal ellipsoids, space filling models, packing and polymeric structures, and 3D real-time rotation of a wire model.
  

The program should have the ability to read and convert Protein Data Bank coordinates to compatible format.

A pipeline, automating the entire work-flow from crystal quality evaluation to data processing and scaling, structure solution, refinement and structure check for organic and coordination compounds shall be included. The routine shall automatically check for major crystallographic pitfalls and avoid these. It shall call established structure solution modules, such as SHELX, automatically to solve the structures, and automatically employ multiple methods for structure solution if the default method is not successful. Atom assignment and verification shall utilize a data base of known structures from organic and metal-organic chemistry.

Info:

The Bruker suite includes unique software to solve and refine protein structures. The system has proven capability to screen protein crystals and collect, integrate and scale data on protein crystals. Software is further able to solve protein structures by ab initio methods in SAD phasing, to locate heavy atom positions, and to trace main protein chains in software which is currently not available to the general public. The proprietary software includes a structure determination method for resolution enhancement by dual-space refinement. This new method remarkably adds 0.2 A to 0.3 A to the resolution of the data, when solving structures of crystals that diffract originally to about 1.8 Angstrom resolution or better.

Agilent by default runs in an automated mode similar to XPRESSO. The software pretends to be hard-working, although results often are very poor. For structure assignment AutoChem is offered, which is a clone of AUTOSTRUCTURE.

Rigaku claims to have SM-Auto and SM-Expert. Very little information is provided on its capabilities.

Tools required for system alignment shall be included with the system.

16. Computer for Instrument Control and Data Processing

17. SUPPORT

Spare parts shall be stocked at the factory as well as in major service centers with provisions in place for same-day shipment.

The ability to provide technical support shall be demonstrated by provision of a list of applications scientists with experience in the crystallography of small molecules using the system offered.

The ability to provide field service shall be demonstrated by provision of a list of field engineers in our region who are trained to install and support the system’s technology.

While the system is under warranty the vendor shall provide a phone number for free-of-charge hot line support with phone-costs covered by the buyer.

The vendor shall grant access to an active electronic systems’ user groupto quickly address daily research problems in the single crystal X-ray diffraction. The access should be at no extra cost. Tenderers shall indicate how many membershave inscribedworldwide.

The vendor shall organize global and local users’ meetings on at least an annual basis for the presentation of new techniques and discussion of novel applications.

Telephone and E-mail support from SC-XRD service experts shall be provided while the system is under warranty. Additional supplier’s support using modern internet tools, such as webex ® for providing tips or showing novel features is a pro. Software and hardware manuals shall be regularly updated and available for download all time.

18. Electrical Power Requirements

This is the standard in Europe, China, India, US and many other countries 16A or 20A circuit breakers are required. For the optional LT device a second, separately fused circuit is required.

19. Low temperature device (option)

Product Sheet SC-XRD 45 KRYOFLEX II Low Temperature Attachment, DOC-S86-EXS045

20. Training