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Figure 1
Common annotations and unit operations used during ISOLDE simulations. (a, b) Cis peptide bonds (marked with asterisks) are filled with a red trapezoid, while twisted peptide bonds (not shown) are filled in yellow. Cα atoms are coloured according to their current Ramachandran status, with outliers (arrowheads) appearing in maroon, marginal conformations shaded from maroon to yellow and preferred conformations shaded from yellow to green with increasing probability. Scripted cistrans and peptide-plane flips act on the peptide bond N-terminal to the selected residue. (c, d) Flipping a peptide plane involves imposing temporary restraints on the φ and ψ dihedrals. Dihedral restraints are annotated by a ring-and-posts motif around each axial bond (marked with daggers), where the angle between the posts gives the current deviation from the target and the colour denotes the level of satisfaction of the restraint. (e, f) Secondary-structure restraints combine φ and ψ restraints, with distance restraints between On and Nn+4 and between Cαn and Cαn+2 displayed as purple dotted pseudobonds (marked with double daggers). (g, h, i) Previews of rotamer options (marked with section symbols) are shown in a thinner stick representation and cycle in order of probability for the given secondary structure. The chosen rotamer coordinates may be committed directly, but it is generally preferable to instead apply the target as dihedral restraints, allowing the atoms to approach the target conformation smoothly without risking clashes. Any heavy atom may be restrained to a given location with a user-defined spring constant (j) and/or tugged directly with the mouse or a three-dimensional input device (k). All panels are screen captures taken from the ISOLDE environment during rebuilding of the MCM2-7 model.

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ISSN: 2059-7983
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