Angle between domains
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| Type | Python Module |
|---|---|
| Download | orientation.py |
| Author(s) | Thomas Holder |
| License | BSD-2-Clause |
|
Included in psico | |
| Module | psico.orientation |
|---|---|
angle_between_domains calculates the rotation and displacement that would happen when aligning two atom selections. The typical use case is for two conformations of a multi-domain structure, which is first aligned on domain 1 (e.g. chain A), and then angle_between_domains is calculated for domain 2 (e.g. chain B).
Usage
angle_between_domains selection1, selection2 [, method
[, state1 [, state2 [, visualize ]]]]
Arguments
- selection1 = str: atom selection in conformation 1
- selection2 = str: atom selection in conformation 2
- method = str: alignment command like "align", "super" or "cealign" {default: align}
Example
# import the "angle_between_domains" command
run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py
# two conformations of a two-chain structure
fetch 1ake, s1, async=0
fetch 4ake, s2, async=0
# align on chain A
align s1 & chain A, s2 & chain A
# measure rotation and displacement of chain B
angle_between_domains s1 & chain B, s2 & chain B
For 1ake and 4ake, this reports:
Angle: 15.55 deg, Displacement: 56.08 angstrom