Software: Easy electron density maps, protein crosslinks, simplified for educators, etc.

Eric Martz • August 24, 2021
Software: Easy electron density maps, protein crosslinks, simplified for educators, etc.
A new version of FirstGlance in Jmol http://FirstGlance.Jmol.Org (free and open source as always) provides guided visual exploration of macromolecular structures with remarkable ease of use (no command language needed). The "FirstGlance" it offers is maximally informative.

This new version should help to de-mystify electron density maps by making them super easy to look at – both for X-ray, and for Electron Microscopic Coulombic density maps. You simply "Find" a few residues (click "Find.." in the Focus Box and, for example, with 1ijw enter Ser174,DA10) which identifies them with yellow halos, whereupon the density map is just one more click. See slides 5-6 showing FirstGlance-generated animations of density maps at http://tinyurl.com/movingmolecules.

Density Maps: https://proteopedia.org/w/Density_maps

Molecule Information Tab: https://bioinformatics.org/firstglance/fgij/where.htm#mit

Focus Box: https://bioinformatics.org/firstglance/fgij/where.htm#focusbox

For educators and students, this new version starts up in a simplified mode, with fewer details cluttering the Molecule Information Tab and hiding advanced tools in the Tools tab. Still, much is offered about the model, including reliability (Rfree interpreted for you), number of chains and which are sequence-identical, sequences, missing residues, full names of ligands, and the biological assembly. The Views Tab shows secondary structure, hydrophobic cores, charge distribution, etc. The Tools Tab shows protein crosslinks, ends of chains, salt bridges, cation-pi interactions, and non-covalent interactions with any moiety you specify.

Click "Show More Details" only if you want detailed analyses of alternate locations (which can be animated) and occupancies, counts of incomplete sidechains, various protein crosslinks, related PDB entries, one-click access to view the PDB data file contents, coloring by temperature/B factor, etc.

This version automatically detects likely cases of the following covalent protein crosslinks (in addition to disulfide bonds, already in FirstGlance for years): isopeptide crosslinks, thioester crosslinks, thioether crosslinks, ester crosslinks, His-Tyr crosslinks, and Lys-Cys NOS crosslinks (first reported a few months ago). Clicking on one crosslink zooms in and shows it in detail, with the electron density map being one further click. Thanks to Amr A. Alhossary for finding some of the examples.

Example in FirstGlance: https://bioinformatics.org/firstglance/fgij/fg.htm?mol=2xi9

Covalent protein crosslinks: https://proteopedia.org/w/Protein_crosslinks

More examples: https://bioinformatics.org/firstglance/fgij/versions.htm#crosslinks

Even more examples: Click "Protein Crosslinks" in the Tools Tab of FirstGlance, then select a type of crosslink.

Feedback always welcome!

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