superposition_view
Superpose two loaded protein structures and color the mobile one by per-residue shift, revealing where conformational changes occur rather than only overall RMSD.
Instructions
Superposes two structures and colors the mobile one by per-residue shift.
An RMSD alone tells you that something moved, not where. This superposes
mobile onto target, measures how far each residue's CA ended up
from its counterpart, and colors the mobile structure blue (unchanged)
through white to red (most shifted). The target is left as a grey
reference cartoon.
Best on two states of the same protein — apo vs holo, open vs closed, a mutant against wild type. Residues are paired by chain and residue number, falling back to residue number alone when the two use different chain IDs.
Both structures have to be loaded first, and fetch_structure clears the
session by default — so fetch the second one with replace=False or it
will replace the first. If either entry is a multimer, compare single
chains (create one object per chain): superposing one dimer onto
another fits the assembly rather than the fold, which inflates the RMSD
dramatically. 4AKE against 1AKE gives 18.5 A as deposited dimers and
2.1 A chain-to-chain.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| method | No | "super" (default) is sequence-independent and handles low identity or different folds; "align" uses a sequence alignment first and is better for near-identical sequences. | super |
| mobile | Yes | Object to move and color (e.g. "1ake"). | |
| target | Yes | Object to superpose onto and leave in place (e.g. "4ake"). | |
| max_deviation | No | Angstrom value mapped to full red. Defaults to the largest observed shift, which maximises contrast; set it explicitly to compare two different pairs on one scale. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |