New capabilities of FirstGlance in Jmol

M
m0lviz@yahoo.com
Wed, Aug 28, 2024 6:50 PM

Firstglance in Jmol (http://firstglance.jmol.org, a general purpose viewer & analyzer for macromolecules, free and open source) has many unique capabilities and conveniences not found in other viewers. These are now listed. The name "FirstGlance" refers to the initial view being as informative as possible (see design goals described at YouTube).

New capabilities include:

  • Spreadsheet-ready lists of atoms contacting any specified moiety, for sorting and averaging. These include bond types, interatomic distances, and (when the PDB file is pre-processed by the ConSurf Server), conservation values. Example. (Visualization of contacts has been available for many years.) Spreadsheet-ready lists of all salt bridges. Example. Spreadsheet-ready lists of atoms found with the Find dialog.

  • New links show electrostatic potential maps that are generated externally by iCn3D. Examples.

  • Backbone "forks" (alternate locations of backbone atoms) are now initially obvious, and can be animated. Examples.

  • It has long been easy to make simple, Powerpoint-ready rocking animations of any view with a few mouse clicks (examples: https://tinyurl.com/movingmolecules ). Instructions are now provided for capturing more complex movies of anything you do in FirstGlance. Sample movies.

  • Complete list of all improvements.
    Since August, 2022:

  • Very large assemblies (biological units), such as virus capsids, clathrin cages, & bacterial gas vesicle tubes are automatically displayed and simplified to facilitate visualization of their gross anatomies. Examples.

  • Unusual covalent protein crosslinks, such as isopeptide bonds and 4 other types, are automatically reported. Clicking on a link to one zooms in and shows it in detail. New YouTube demonstation.
    -Eric
    Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his)
    U Mass, Amherst -- Martz.MolviZ.Org

  • Guided Exploration of Macromolecules: FirstGlance.Jmol.Org

  • Protein 3D Structure Wiki: Proteopedia.Org

  • Top Five 3D MolVis Tools: Top5.MolviZ.Org

  • Education: Biochem in 3D at MolviZ.Org

  • YouTube Channel

  • Find Functional Patches in Proteins: ConSurf

  • Atlas of Macromolecules: Atlas.MolviZ.Org

  • Interactive Molecules in Architectural Spaces: MolecularPlayground.Org

  • Workshops: Workshops.MolviZ.Org

Firstglance in Jmol (http://firstglance.jmol.org, a general purpose viewer & analyzer for macromolecules, free and open source) has many unique capabilities and conveniences not found in other viewers. These are now listed. The name "FirstGlance" refers to the initial view being as informative as possible (see design goals described at YouTube). New capabilities include: - Spreadsheet-ready lists of atoms contacting any specified moiety, for sorting and averaging. These include bond types, interatomic distances, and (when the PDB file is pre-processed by the ConSurf Server), conservation values. Example. (Visualization of contacts has been available for many years.) Spreadsheet-ready lists of all salt bridges. Example. Spreadsheet-ready lists of atoms found with the Find dialog. - New links show electrostatic potential maps that are generated externally by iCn3D. Examples. - Backbone "forks" (alternate locations of backbone atoms) are now initially obvious, and can be animated. Examples. - It has long been easy to make simple, Powerpoint-ready rocking animations of any view with a few mouse clicks (examples: https://tinyurl.com/movingmolecules ). Instructions are now provided for capturing more complex movies of anything you do in FirstGlance. Sample movies. - Complete list of all improvements. Since August, 2022: - Very large assemblies (biological units), such as virus capsids, clathrin cages, & bacterial gas vesicle tubes are automatically displayed and simplified to facilitate visualization of their gross anatomies. Examples. - Unusual covalent protein crosslinks, such as isopeptide bonds and 4 other types, are automatically reported. Clicking on a link to one zooms in and shows it in detail. New YouTube demonstation. -Eric Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) U Mass, Amherst -- Martz.MolviZ.Org - Guided Exploration of Macromolecules: FirstGlance.Jmol.Org - Protein 3D Structure Wiki: Proteopedia.Org - Top Five 3D MolVis Tools: Top5.MolviZ.Org - Education: Biochem in 3D at MolviZ.Org - YouTube Channel - Find Functional Patches in Proteins: ConSurf - Atlas of Macromolecules: Atlas.MolviZ.Org - Interactive Molecules in Architectural Spaces: MolecularPlayground.Org - Workshops: Workshops.MolviZ.Org