Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several modeling tools into UCSF Chimera. These include comparative modeling by MODELLER, simultaneous fitting of multiple components into electron microscopy density maps by IMP MultiFit, computing of small-angle X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera.
Bibliographical noteFunding Information:
The authors gratefully acknowledge Prof. Wah Chiu and Dr. Steven Ludtke for providing the SAXS experimental data for the GroEL example. The research of K. Lasker was supported by continuous mentorship from Prof. Haim J. Wolfson as well as a fellowship from the Clore Foundation Ph.D. Scholars program . K. Lasker’s research was carried out in partial fulfillment of the requirements for a Ph.D. degree from TAU. This work was funded by NIH Grants R01 GM083960 , U54 RR022220 , and PN2 EY016525 to A. Sali and P41 RR001081 to T.E. Ferrin.
- Electron microscopy
- Integrative structural modeling
- Interactive molecular visualization
- Restraint-based modeling
- Small-angle X-ray scattering