Improved SC-XRD Models with Bruker IDEAL (Invariom Derived Electron AnaLysis)

How to achieve better crystallography models with IDEAL (Invariom Derived Electron AnaLysis), part of Bruker’s APEX3 SC-XRD software.

Blue Scientific is the official Nordic distributor for Bruker SC-XRD instruments in Norway, Sweden, Denmark, Finland and Iceland. For more information or quotes, please get in touch.

Bruker SC-XRD range

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Bruker IDEAL

IDEAL (Invariom Derived Electron AnaLysis) is part of Bruker’s APEX3 SC-XRD software. It extends the classic Independent Atom Model (IAM) to aspherical atom models:

  • Model bond and lone-pair density.
  • More accurate structure models.
  • Significantly improved bond precision
  • Reduced residual densities.
  • Identify incorrect atom assignments and missed atoms or disorder, even in metal complexes.
  • Potential tool for structure validation.
SC-XRD Fragment Assignment
Automatic or manual fragment assignment using IDEAL, with instant visual feedback.

Limitations of Standard Methods

The Independent Atom Model (IAM) is a standard crystallography method that uses spherical scattering factors to model atoms in structures from X-ray diffraction data. However, it was developed in the past when the capabilities of XRD instruments were very limited.

It oversimplifies the description of electron densities, because the charge cloud of an atom is rarely spherical – the shape is deformed by nearby atoms, bonds and lone pairs. In charge density analysis, these phenomena have been described with elaborate multipole models that simulate charge distribution.

Careful data acquisition is necessary to achieve the data quality and high resolution required. Experiments are lengthy, and the process of establishing and refining meaningful multipole models is a extremely time-consuming. In the past, technology was less capable and measurement times were long, even for high quality crystals. This meant that experiments were usually limited to lower resolutions, which justified the use of the IAM.

Get the Most from Your Data

Today, SC-XRD technology is far more advanced: with large photon-counting detectors and high-brilliance X-ray sources, you can routinely collect precise, high resolution data from short experiments.

Make the most of this superior data with Invariom Derived Electron AnaLysis (IDEAL):

  • Expands the IAM to aspheric atom models, using scattering contributions from bonds and lone pairs.
  • Improves structure models significantly, making full use of the data collected.
  • Easy to use within the APEX3 software suite.
  • Fully integrated with the IUCr’s checkCIF routines.

With IDEAL, you can easily improve refinement results, with significantly smaller residual densities and more precise bond lengths. It makes it much easier to identify missing and incorrectly assigned atoms. This then makes it easier to model disordered segments.

Residual electron density map of Alanine
Residual electron density map of Alanine. The IAM refinement clearly shows bonding density and oxygen lone pairs, and in the IDEAL refinement the density is nicely modelled.


See the difference IDEAL makes in Bruker’s application note, which walks you through the process and compares the structure refinement of various compounds with IAM and IDEAL:

Download the application note

Bruker SC-XRD Range

IDEAL is an add-on to Bruker’s APEX3 crystallography software for structure determination, covering the entire process from sample centring to publication-ready reports. PEX3 is the dedicated software suite for Bruker’s entire SC-XRD range.

APEX3 Brochure

Bruker APEX3 Crystallography Software
Bruker APEX3 Crystallography Software
Bruker D8 VENTURE 2nd Generation


  • Most versatile – configure for any SC-XRD application (biological or chemical).
  • All dual wavelength combinations.
  • Best-in-class components.
  • Open design; modular system with room for expansion.

Bruker D8 QUEST - 2nd Generation

Bruker D8 QUEST

  • Single wavelength experiments.
  • Compact, small footprint system.
  • Best-in-class components.



  • Energy-efficient version consuming fewer resources.
  • Low cost of ownership .
  • Single source.
  • Full-featured research instrument offering best-in-class performance.

More Information

Blue Scientific is the official distributor of Bruker SC-XRD in the Nordic region. We’re available to answer all your questions – just get in touch:

 Contact us on +44 (0)1223 422 269 or

 Bruker X-Ray Analysis range