ChimeraX, a new version of Chimera available on SBgrid


Introduction

UCSF Chimera is one of the most popular molecular viewer. It is currently developed by the Resource for Biocomputing, Visualization, and Informatics at University of California, San Francisco. Among its many features, Chimera is probably the best software for the interactive visualisation and analysis density maps. It allows for a fine-tuning of the density maps and provides built-in algorithms for the rigid fitting of atomic structures into the map.

We focus here on the brand new version of the software, Chimera X, which aims at redesigning the software interface and comes with new advanced features addressing the new needs of the community [1].

What’s new

We appreciate the integration of HTML pages that can contain ChimeraX commands usable as links to run any action in the software. This feature allows to easily share any pipeline or tutorial that would mix commands and illustrations.

Creating morphing videos has never been that easy and a simple morphcommand allows you to easily create an animation to show the conformational changes in your favorite structure.

You want to print this structure in 3D? Then use thestrutscommand and create pseudo-bonds to rigidify the structure before printing.

In parallel, a lot of efforts have been made to improve the rendering quality of molecular scenes. Integration of ambient occlusion significantly improves the rendering and curved helix representation gives an interesting new perspective into the secondary structure elements of macromolecules.

Integrative/Hybrid methods support

But perhaps the most relevant new feature of ChimeraX for our community is its support for mmCIF files, which can be generated by Integrative Modelling and Hybrid methods (IM/H methods). This allows the visualisation of multi-scale, multi-state and time-ordered ensembles of macromolecular assemblies. Noteworthy, this is in line with the recommendations and developments made by the wwPDB task force for the archiving and visualisation of models coming from hybrid methods [2]. Their recent efforts resulted in an extension of the PDBx/mmCIF format by the addition of a new data dictionary. This dictionary addresses two fundamental requirements of IM/H methods: (a) descriptions of spatial restraints derived from a variety of experimental techniques and (b) definitions of multi-scale, multi-state, and time-ordered ensembles of macromolecular assemblies. A general representation of multi-scale models, together with the experimentally determined spatial restraints, is an important feature of this new mmCIF format.

A recent webinar, organised by the SBgrid consortium, went over most of these new features.

ChimeraX is under active development and new features are expected to be released on a regular basis, you can monitor the change log here.

SBgrid consortium

Chimera X can be downloaded directly on the UCSF website but is also distributed within the SBgrid consortium [3]. SBgrid supports structural biologists by maintaining a large library of scientific applications. Members of the consortium get access to this repository as well as support, training and HPC resources. Currently, SBgrid gathers 387 scientific software – including former versions of most of them – available both on Linux and OSX platforms.

Beyond software, SBgrid also provides a Data Bank where X-ray diffraction, MicroED, LLSM datasets, as well as structural models can be deposited. Each accepted dataset receives a DOI and is therefore citable and easily accessible from any scientific communications.

To join the consortium you can fill in the form here.

References

[1] Goddard, T.D. et al. “UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis.Protein Science (2017)
[2] Sali, Andrej, et al. “Outcome of the first wwPDB hybrid/integrative methods task force workshop.” Structure 23.7 (2015): 1156-1167.
[3] Morin, A. et al. “
Cutting Edge: Collaboration gets the most out of software.eLife (2013)

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