How is core.find different from sieve fit method

[Former user]

Hi,

I would like to know how is the core.find function which uses volume description to find structural core different from the sieve-fit method which uses rmsd 0.5A..

Moreover is it possible to perform all atom NMA in bio3d and write an all atom NMA trajectory.

Is it possible to perform pca on structures aligned using other structural alignment programs.

[Barry Grant]

Thanks for your question. Which 'sieve-fit method' are you referring to exactly?

Briefly the core find procedure employs iterated rounds of structural superposition to identify the most structurally invariant region. This procedure entails excluding those residues with the largest positional differences (measured as an ellipsoid of variance determined from the Cartesian coordinates of equivalent Cα atoms), before each round of superposition, until only the invariant “core" residues remain.

All-atom NMA is not in the current package version but is on the To-Do list - thanks for registering your interest in this.

[Lars Skjærven]

A preliminary version of all-atom ENM is available in the feature_aanma branch.