Chimera Plug-ins on the Web

TALAIA: simplified 3D protein representations

August 8, 2023

TALAIA represents different types of amino acid residues as simplified objects with different shapes and colors, to facilitate rapid recognition of molecular properties and types of interactions. TALAIA is described in Alemany-Chavarria et al., Bioinformatics 39:btad476 (2023).

SINAPs: Comparing Interaction Networks

SINAPSs (Structural Interaction Network Analysis Protocols) compares the interaction networks of two atomic structures or two trajectories, with similarities and differences shown using a Chimera plugin. See Bedart et al., J Chem Inf Model 62:1425 (2022).

RNArtist: design RNA structure in 2D, explore in 3D

March 4, 2021

RNArtist allows designing RNA 2D structures interactively and using UCSF Chimera (or UCSF ChimeraX) to explore 3D architectures. RNArtist is developed by Fabrice Jossinet at the University of Strasbourg. See also: Assemble2

MAINMAST-GUI: Protein Modeling from cryoEM

The MAINMAST-GUI Chimera plugin is a graphical interface for building protein atomic structures into cryoEM maps with MAINMAST. See Terashi et al., Methods Mol Biol 2165:317 (2020).

MapQ: Atom Resolvability in cryoEM Maps

MapQ evaluates atom resolvability in cryoEM maps. See Pintilie et al., Nat Methods (2020). See also: ModelZ

Sophia: Learning Molecular Simulations

December 19, 2019

Sophia is an interactive teaching and learning tool for small-scale molecular simulations. It was developed by Geoff Rollins as a plugin to Chimera, primarily on MacOS, with some but not all features available if used on Windows or Linux. Detailed documentation is available, with examples (argon and alanine simulations) and several tutorials (harmonic oscillator, small clusters of Lennard-Jones particles, simulated annealing).

Tangram Modeling Tools

April 16, 2018

The Tangram suite is a collection of molecular modeling tools for UCSF Chimera developed by InsiliChem (JD Maréchal's group, Universitat Autònoma de Barcelona). The tools include simple representations of glycosylation groups, depiction of protein-ligand interactions, protein pKa analysis, substructure alignment, normal mode analysis, visualization of results from docking or conformational search (see GaudiView), setup for MD, QM, and QM/MM calculations, and several others (details...).

PyChimera

April 16, 2018

PyChimera allows using the UCSF Chimera Python API in a standard interpreter. PyChimera is described in Rodríguez-Guerra Pedregal et al., Bioinformatics 34:1784 (2018).

See also: JR Healey's PyChimera scripts

ChimAARON Interface to QM-Related Tasks

The ChimAARON plugin is built upon the Python implementation of AARONTools, a collection of tools for automating routine tasks associated with running quantum chemistry calculations with Gaussian. See Guan et al., J Chem Theory Comput 14(10):5249 (2018).

Protein Structure Validation Tool for cryoEM

The ECSU Label plugin for Chimera shows outliers in protein φ, ψ, χ₁ angles and other geometric descriptors, as described in Chen et al., Medicines 6(3):86 (2019). The plugin is available from GitHub.

Secondary Structure from Cryo-EM: SSETracer, StrandTwister

SSETracer, StrandTwister, and AxisComparison are tools for identifying secondary structure from cryo-EM maps. They can be used from within Chimera (details and download). Developed by the Jing He lab and collaborators. See also Haslam et al., Bioinformatics Research and Applications. ISBRA 2018. Lecture Notes in Computer Science, vol 10847. Springer (2018).

ModelZ: Z-score Evaluation of Features in cryoEM Maps

ModelZ evaluates how well sidechains and secondary structure elements are resolved in cryoEM density maps. See Pintilie and Chiu, J Struct Biol 204:564 (2018). See also: MapQ

CHEWD: Residue Contributions to Binding Energy

CHEWD (Chemical Energy-Wise Decomposition) is a Chimera plugin for visualizing energy-decomposition output from Amber MM/PBSA molecular dynamics or WaterSwap Monte Carlo simulations. See Raza et al., J Comp-Aided Mol Design 33:461 (2019).

Create BILD Objects in Command Line

December 19, 2017

The Chimera_BILD extension on GitHub implements some BILD commands as Chimera commands. This allows simply using the Chimera command line instead of making an input BILD file to define geometric objects (3D arrows, etc.) in Chimera. Developed by José Emilio Sánchez Aparicio.

EM Fitting Plugins

September 21, 2017

ADP_EM is an ultrafast multiresolution rigid-body fitting tool, described in Garzón et al., Bioinformatics 23:427 (2007). iMODFIT is an efficient tool for flexible fitting into EM maps based on internal-coordinate normal mode analysis, described in Lopéz-Blanco and Chacón, J Struct Biol. 184:261 (2013). Both fitting programs and their respective Chimera plugins [ADP_EM plugin] [iMODFIT plugin] are developed by the Chacón lab at the Rocasolano Physical Chemistry Institute in Madrid, as part of its focus on hybrid methods.

Pre- and Post-Processing for DFT Calculations

August 23, 2017

Tetr and Lev00 are pre- and post-processing tools, respectively, for DFT codes including CP2K (Lev Kantorovich, King's College, London). Tetr assists setting up a system geometry, whereas Lev00 can calculate phonons and IR intensities, compute the electronic density of states, and display charge and spin densities. These programs run on UNIX-based operating systems, not MS Windows. The CP2K-UK project (EPSRC grant EP/K038583/1) has developed a plugin that allows Tetr and Lev00 to run coupled to Chimera for interactive visualisation and atom selection.

MOLE 2.5

July 20, 2017

The MOLE 2.5 plugin to Chimera allows exploration and analysis of channels, tunnels and pores within biomacromolecules. Channel profiles and physicochemical properties are reported. Documentation and plugin download (which includes the MOLE binary) are available from the MOLE website. On platforms other than Windows, Mono must also be installed. MOLE is described in Sehnal et al., J Chemoinf 5:39 (2013) and is developed by the WebChemistry group at the Czech Republic National Centre for Biomolecular Research.

ValidatorDB

July 20, 2017

The ValidatorDB plugin to Chimera accesses a database of validation information for all ligands and nonstandard residues in Protein Data Bank structures. Discrepancies such as missing atoms, incorrect chiralities, and naming convention violations are reported. The plugin is available at the ValidatorDB website. ValidatorDB is described in Sehnal et al., Nucleic Acids Res 43:D369 (2015). The database and associated plugin are developed by the WebChemistry group at the Czech Republic National Centre for Biomolecular Research.

GaudiView: Explore Results from GaudiMM and GOLD

April 20, 2017

The GaudiView plugin to Chimera is a light interface to explore and analyze solutions from GaudiMM modeling and/or GOLD docking. GaudiView and GaudiMM are developed by InsiliChem (JD Maréchal's group, Universitat Autònoma de Barcelona). GaudiMM is described in Rodríguez-Guerra Pedregal et al., J Comput Chem 38:2118 (2017).

GPathFinder: Identify and Display Ligand Binding Pathways

August 11, 2019

GPathFinder is an extension built over the GaudiMM core (see above) for the calculation and display of ligand binding pathways. GPathFinder is described in Sánchez-Aparicio et al., Int J Mol Sci 20:3155 (2019).

LocalFSC: estimate local resolution in an EM map

September 21, 2016

The LocalFSC plugin to Chimera estimates the resolution in selected subregions of an EM map. Resolution is estimated by Fourier Shell Correlation (FSC) using two independent maps, such as from disjoint subsets of the data. Selection is performed by placing markers in the regions of interest. The method and plugin are described in Cardone et al., J Struct Biol 184:226 (2013). See also: ResMap

ProBiS: prediction of binding sites and ligands

August 26, 2016

The ProBiS plugin connects Chimera to a web database of pre-calculated binding site comparisons and enables viewing the predicted binding sites and corresponding ligands in 3D. See also the ProBiS server.

3DIANA: 3D domain interaction analysis

March 9, 2016

3DIANA is a web-based environment that integrates low-resolution density maps, atomic structures, homology, and predictions of domain-domain interactions to model quaternary structure. Results are accessible through a web browser or a Chimera plugin. 3DIANA is described in Segura et al., Biophys J 110:766 (2016).

Xlink Analyzer: protein crosslinking for structure characterization

February 19, 2015

Xlink Analyzer is a tool for the visualization and analysis of protein crosslinks and their consistency with spatial restraints. It is implemented as a Chimera plugin by the Martin Beck group (EMBL, Heidelberg) and described in Kosinski et al., J Struct Biol 189:177 (2015).

PyRy3D: building low-resolution models of large complexes

June 18, 2013

The PyRy3D Chimera extension provides a graphical interface to PyRy3D, a method for building low-resolution models of large macromolecular complexes using Monte Carlo simulations with spatial restraints. The components can be represented as rigid bodies or as flexible shapes. PyRy3D is developed by Joanna M. Kasprzak, Wojciech Potrzebowski, Mateusz Dobrychłop, and Janusz M. Bujnicki in the Laboratory of Structural Bioinformatics, Adam Mickiewicz University, Poznan.

Assemble2: design RNA structure in 2D, build in 3D

Dec 18, 2012

Assemble2 allows designing 2D RNA structures interactively and generating corresponding 3D structures in Chimera. It uses web services for RNA structure prediction and refinement. Executables, source code, and documentation are available for download. Assemble2 is developed by Fabrice Jossinet (now at the University of Strasbourg). See also: RNArtist

SwissSidechain: non-natural amino acids

Dec 1, 2011

The SwissSidechain Chimera module allows mutating amino acids into non-natural residues found in the SwissSidechain database, using a Rotamers-type interface or an additional command, swapnaa. The database includes rotamers for > 200 non-natural residues (browse...). The module and database are developed by David Gfeller, Olivier Michielin, and Vincent Zoete in the Swiss Institute of Bioinformatics Molecular Modelling Group.

Viewer for psc++-calculated pairwise/multiple alignments

July 27, 2009

PscViewer facilitates the calculation and visualization of pairwise and multiple structure-based alignments. PscViewer is mainly an interface to the psc++ structure alignment program but also supports display of structure alignments if specified in a certain XML-based format. PscViewer contains three tools:

1. Create/View Psc++ Alignment to calculate and view alignments.
2. Load XML file to load and display precalculated alignments stored in a certain XML format.
3. Load Database Search to load a ranked list of hist in a structure database given a certain query and subsequently to calculate the corresponding pairwise alignment. The ranked list data can be derived with psc++.

Viewer for 3D motif matches from LabelHash

April 24, 2009

The LabelHash Server searches the PDB for matches to a user-specified 3D motif (pattern of residues). The authors provide the Chimera extension ViewMatch for looking through the hits superimposed on the query. LabelHash can also be downloaded for local command-line use. LabelHash and ViewMatch are provided by the Kavraki Lab at Rice University.

Slice viewer for electron tomography

April 3, 2007

TomoPlane displays slices of electron tomography data sets oriented at arbitrary angles. Developed by Karin Gross and Christoph Best at Max Planck Institute for Biochemistry.

Predict non-linear optical properties of molecules

April 3, 2007

NLOPredict predicts and analyze non-linear optical properties of molecules. Developed by in a collaboration between the lab of Garth Simpson at Purdue University and Charlie Moad and Randy Heiland at the Scientific Data Analysis Lab, Indiana University.

Animation Editor

April 3, 2007

EMANimator creates animations of electron microscope maps and molecular models using a graphical timeline interface. Supports model motions, model color changes, showing and hiding models, changing thresholds for isosurfaces, and camera zooms. Developed by Steve Ludtke at Baylor College of Medicine.

View NMR assignments on a molecular structure

April 3, 2007

The Sparky molecule view extension displays NMR assignments and distance constraints from the NMR assignment program Sparky on a molecular structure. Developed by Tom Goddard at the University of California at San Francisco.