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Resources: Guided Molecular Visualization: FirstGlance v. 3.0 Released
Submitted by Eric Martz; posted on Friday, April 10, 2020
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FirstGlance in Jmol (http://firstglance.jmol.org – or google firstglance as one word (no space) – free and open source) provides guided macromolecular visualization with remarkable ease of use and extensive help. Designed for educators and students, nevertheless it has ample power for researchers. Non-technical language abounds. For example, the B-factor/temperature color scheme is labeled "Local Uncertainty" (with the technical terms in the explanation). Resolution, reliability, asymmetric unit, biological assembly, etc. are explained in plain language. Any view can be easily saved as a rocking animation for presentation slides or websites (http://tinyurl.com/movingmolecules).
- The name "FirstGlance" refers to a maximally informative initial view. Each chain is a distinct pastel color. Missing residues are marked with "empty baskets" so you won't be unaware (examples: 6NJE http://firstglance.jmol.org/fg.htm?mol=6nje and 2ho3 http://firstglance.jmol.org/fg.htm?mol=2ho3). Missing sidechains are labeled "S-", D-amino acids "D", non-standard residues "X". Full names of ligands are listed, clickable to locate each in the 3D structure.
- Fundamental features such as secondary structure, distributions of hydrophobic/polar residues and charges, disulfide bonds, salt bridges, cation-pi interactions and more can be seen with one click each. Color keys and help appear automatically. All protein-protein salt bridges (including those involving ends of protein chains) can be listed, spreadsheet ready (example listing https://bioinformatics.org/firstglance/fgij/1hxw-salt-bridges.htm for 1HXW http://firstglance.jmol.org/fg.htm?mol=1hxw).
- Components of a structure can be hidden to simplify the view, just by clicking on them. They remain hidden in all other views until explicitly re-displayed.
- Any single chain or compound, or range of residues, can be isolated (everything else hidden) with one or a few clicks.
- A powerful "Find" mechanism highlights short sequences, ranges of sequence numbers, residues by name, chemical elements, etc. Contacts and non-covalent bonds with whatever you find are easily displayed. Found items can be isolated or hidden.
- You can select any component and then see what is non-covalently (or covalently) bound to it in just a few clicks. Seven categories of non-covalent interactions with your designated target can be shown, one at a time.
- Reliability (Rfree) is objectively graded and explained. Date of publication, resolution, sequences, source organisms, molecular mass, chemical elements in the model, publication abstract are readily viewed. For the more advanced user, alternate locations can be animated with a few clicks (example: 2AGT http://firstglance.jmol.org/fg.htm?mol=2agt – click on alternate locations in the Introduction), occupancies less than 100% are summarized and easily located, and regions of the asymmetric unit with crystal contacts can be colored.
FirstGlance is used about 300 times/day.
I'm always interested in feedback, problems, bug reports, suggestions or questions.
Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) U Mass, Amherst – http://Martz.MolviZ.Org
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