A new version of FirstGlance in Jmol http://firstglance.jmol.org is
released. Shift-Reload or clear the cache in your browser to ensure you
are using version 3.51.
It should help to de-mystify electron density maps
https://proteopedia.org/w/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 https://proteopedia.org/wiki/fgij/where.htm#focusbox, and
for example with 1ijw enter Ser174,DA10), whereupon the density map is
just one more click. Bob Hanson was a huge help, making simple Jmol
commands do a lot of work behind the scenes. See slides 5-6 showing
FirstGlance-generated animations of density maps at
tinyurl.com/movingmolecules http://tinyurl.com/movingmolecules.
For educators and students, this new version starts up in a simplified
mode, with less details cluttering the Molecule Information Tab and
hiding advanced tools in the Tools tab. Thanks to Gabriel Pons for
motivating me to do this.
Click "Show More Details" only if you want detailed analyses of
alternate locations (which can be animated
https://proteopedia.org/w/Alternate_locations#Visualizing_alternate_locations)
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
https://proteopedia.org/w/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. Examples
https://proteopedia.org/wiki/fgij/versions.htm#crosslinks. Thanks to
Amr A. Alhossary for finding some of the examples.
Feedback always welcome! -Eric
Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his)
Univ. Massachusetts, Amherst -- Martz.MolviZ.Org http://martz.molviz.org/
Guided Exploration of Macromolecules with Powerpoint-Ready Animations:
FirstGlance.Jmol.Org http://firstglance.jmol.org/
Protein 3D Structure Wiki: Proteopedia.Org
http://proteopedia.org/w/User:Eric_Martz
Education: Biochem in 3D at MolviZ.Org http://molviz.org/
Find Functional Patches in Proteins: ConSurf.tau.ac.il
http://consurf.tau.ac.il/
Atlas of Macromolecules: Atlas.MolviZ.Org http://atlas.molviz.org/
See multiple protein sequence alignments clearly: MSAReveal.Org
http://msareveal.org/
Pockets And Cavities Using Pseudoatoms in Proteins: PACUPP
http://molviz.org/pacupp
Interactive Molecules in Architectural Spaces: MolecularPlayground.Org
http://molecularplayground.org/
Syllabi: Workshops.MolviZ.Org http://workshops.molviz.org/