SAFIR is a program for interactive rigid-body modelling into low-resolution shapes restored from small-angle scattering data. The program has been designed with an emphasis on ease of use and intuitive handling. An embedded version of MolScat or external software such as CRYSOL can be used to evaluate of the fit between the model and experimental scattering data. SAFIR also provides options to refine macromolecular complexes with optional user-specified restraints against scattering data by means of a Monte-Carlo approach.
- Intuitive and convenient handling
- Jmol molecular viewer
- Built-in MolScat module for evaluation of the solution scattering of models
- Wrapper for CRYSOL 3 as an external module to evaluate the solution scattering of models (requires installation of the ATSAS package)
- Extraction of protein rigid bodies from PDB files based on chain identifiers
- Superposition of SAXS-derived low-resolution shapes
- Manual adjustments of atomic models as Cα traces through key-driven movements
- Clash check of models
- Monte-Carlo rigid body refinement
Interactive model adjustment and superposition of low-resolution shapes using a Jmol molecular viewer panel
Model adjustments are possible by transformation of selected rigid bodies:
| Keystroke | Translation | Rotation |
|---|---|---|
| NumPad 8 or UP arrow | positive z-translation (up) | rotation around x-axis |
| NumPad 2 or DOWN arrow | negative z-translation (down) | rotation around x-axis |
| NumPad 6 or RIGHT arrow | positive x-translation (right) | rotation around z-axis |
| NumPad 4 or LEFT arrow | negative x-translation (left) | rotation around z-axis |
| NumPad 9 | positive y-translation (to the back) | rotation around y-axis |
| NumPad 1 | negative y-translation (to the front) | rotation around y-axis |
Evaluation of the solution scattering of the current model and fit to the experimental scattering data
Computation of the pair distance distrubtion function of the current model using the built-in MolScat module
Monte-Carlo refienment of the current model against the experimental scattering data
When using this program, please cite:
Hofmann, A., Whitten, A. (2014) Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules. J. Appl. Crystallogr. 47, 810-815.