ISOLDE: Bringing structural biology to life

Features

Interactive restraints

In order to provide more precise control in 3D, ISOLDE allows the quick and easy addition of additional restraints (position, distance and/or torsion) where needed to guide the model smoothly into a desired conformation. Working this way (rather than simply rewriting the coordinates of some subset of atoms) avoids any possibility of introducing problematic clashes and other unphysical geometry, giving an often remarkably wide radius of convergence.

In the video we see, in order of appearance:

  • Dialing up different lysine rotamer previews, then applying them as torsion restraints;
  • Adding position restraints to selected atoms;
  • Applying and adjusting a distance restraint between two atoms;
  • Applying secondary structure restraints (a combination of torsion and distance restraints) to an alpha helix. Notice that when I deliberately disrupt the helix (by applying beta-strand restraints), reapplying alpha-helical restraints returns it nearly to its original position.

New in ISOLDE 1.0b3: Adaptive distance restraints

When working with low-resolution density, it is quite common to encounter the situation where you have a reference model which is similar to yours in its short-range detail, but differs over longer distances due to conformational changes. ISOLDE's adaptive distance restraints (pictured on the left) are designed to help with such cases. These act like simple harmonic restraints when close to their target distances, but beyond a user-defined cutoff they gradually "give up", allowing real large-scale conformational changes to occur while still restraining short-range conformations. This video demonstrates the key step in an interactive tutorial introducing these (accessible from within ChimeraX using the command 'isolde tutorial'), re-fitting the E. coli LptB2FGC complex from its ATP-bound conformation (6mhz) into a 4.0 Angstrom cryo-EM map of its apo state (EMD-9118). Also demonstrated in this video are the new abilities to visualise as C-alpha trace, and to interactively tug on any user-defined selection. "Satisfied" restraints appear as green bars, while overly-compressed and overly-stretched restraints appear in yellow and purple respectively. The thickness of each restraint scales with its applied force.

ISOLDE is developed and maintained by Tristan Croll in the lab of Randy Read at the Cambridge Institute for Medical Research and supported by Prof. Read's Wellcome Trust Principal Research Fellowship 209407/Z/17/Z. Development and testing has been aided by the generous donation of a GTX Titan Xp GPU by NVIDIA Corporation.

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