List of actions available to the ffeatools script.

<p>List of actions available to the ffeatools script.</p

The RMSD traces of the 2 different simulations of GroEL following an RMS fit to the average structure.

<p>The RMSD traces of the 2 different simulations of GroEL following an RMS fit to the average structure.</p

Diagram of the structure of data in FFEA.

<p>The same structure is used both in the “runner” and in the “tools”.</p

Strong scaling plots for a system of 32 GroEL complexes, run using a 32 HT core computer.

<p>a) Execution time b) Speedup.</p

An electron microscopy map of GroEL (EMDB entry EMD-5403) as seen in Chimera [26](left), then converted to “.stl” using the emmaptosurf ffeatool visualised in VMD [27] (centre), and the final volumetric mesh, coarsened so that the shortest edge is 12Å visualised using the FFEA plugin for PyMOL (right).

<p>An electron microscopy map of GroEL (EMDB entry EMD-5403) as seen in Chimera [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005897#pcbi.1005897.ref026" target="_blank">26</a>](left), then converted to “.stl” using the emmaptosurf ffeatool visualised in VMD [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005897#pcbi.1005897.ref027" target="_blank">27</a>] (centre), and the final volumetric mesh, coarsened so that the shortest edge is 12Å visualised using the FFEA plugin for PyMOL (right).</p

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules - Fig 19

<p>a) The two soft, viscoelastic spheres before collision. b) The spheres collide and suffer a large deformation. c) The spheres bounce back as a result of the steric interactions, recover their shape, and experience negligible rotation or deflection. A movie is available in the supplementary <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005897#pcbi.1005897.s003" target="_blank">S3 File</a>.</p

A representation of the 5 most flexible eigenmodes of the GroEL 1GPa model.

<p>A representation of the 5 most flexible eigenmodes of the GroEL 1GPa model.</p

The eigenvalues, which correspond to positional variance, of the 20 most flexible modes found from PCA analysis of a 3<i>μ</i>s FFEA simulations of GroEL.

<p>The eigenvalues, which correspond to positional variance, of the 20 most flexible modes found from PCA analysis of a 3<i>μ</i>s FFEA simulations of GroEL.</p

Weak scaling plots for a system composed of an increasing number of GroEL units matching the number of processors used, up to 248, in a large shared memory machine.

<p>a) Execution time b) Efficiency.</p

The eigenvector inner product matrices between compared trajectories.

<p><b>a)</b> is the comparison between atomistic and FFEA pseudo-atomistic PCA datasets. <b>b)</b> is the comparison between the first and second halves of the atomistic datasets.</p