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Index to FirstGlance in Jmol
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1 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

- 3' end of nucleic acid: See N->C Rainbow.
- 5' end of nucleic acid: See N->C Rainbow.
- %A, %B, etc. Letters preceded by "%" are how Jmol references alternate locations of atoms (alternate conformations). References to %A etc. will appear in the atom identification report when you touch an atom, or click on an atom. For an explanation, load 2agt and click on "alternate locations" in the Introduction or in the Molecule Information Tab.
- Abstract of the publication: Available with an "Abstract" link in the lower portion of the Molecule Information Tab.
- Acknowlegements: See Copyright, Licenses, Acknowledgements.
- ADP ligand
- Adoptions of FirstGlance: Journals and structural bioinformatics resources that have adopted FirstGlance in Jmol are listed at Adoptions.
- Alpha carbon only models
- Alpha helices: See Secondary Structure.
- Alternate locations: (Alternate Conformations.) For an explanation, load 2agt and click on "alternate locations" in the Introduction or in the Molecule Information Tab. You will see a table analyzing alternate locations, including the actual number of locations for each atom that has an alternate location code (locations/atom). You can animate alternate conformations, and find various subsets. See also "%A, %B, etc." at the top of this section. See also Occupancies.
- Amino acid, locating in the molecular view: See Find.
- Amino acids, single (not part of a polypeptide), or lacking alpha carbon atoms, or lacking peptide-bonding atoms, or lacking main chain oxygens
- Amino acids, total number in the model: Given as a count of alpha carbon atoms in the Molecule Information Tab.
- Amino terminus: See N->C Rainbow.
- AMP ligand
- Angles: Use Distances/Angles in the Tools tab.
- Animations: To save an animation, click "Save Image or Animation" (highlighted in orange) below the molecule. These animations (multi-GIFs) can be shown in presentations (Powerpoint, Google Slides, Libre Office, etc.). More information. See also: Images.
- Anionic amino acids: See Charge.
- Anomalous atoms: Atoms shown as dots in the initial view are "anomalous atoms" that do not fit the format standards for a Protein Data Bank data file. To hide these or change the rendering (or for examples), use Advanced/Technical in the Tools tab. Should these ever occur, they
  .
- Assessment plans for educators: See Plans ... under the Resources Tab.
- Asymmetric unit: Shown in the Molecule Information Tab with a link to an explanation.
- Atlas of Macromolecules: See Gallery.
- Atom counts: To get counts of all atoms in a model, open the Molecule Information Tab. Under "Asymmetric Unit" are reports of chemical elements, and hydrogen in the model. Click on either link to get a more detailed report. If you click on elements, you'll get a count of each chemical element. Near the bottom of each explanation is a list H/non-H Atom Counts by Composition.
- Atomic clashes: In the Resources tab.
- Atomic coordinate axes: See Axes.
- ATP ligand
- Authors: Authors of the model are listed in the Molecule Information Tab. Below this list are links to show the abstract of the structure report, and other relevant citations provided in the PDB file.
- Axes for atomic coordinates: The Cartesian coordinate axes can be displayed: use Advanced/Technical in the Tools tab.
- B factor: See Local Uncertainty.
- Back up: See Undo.
- Backbone trace: For proteins, a backbone trace is a line following the positions of alpha carbons (see backbone representations). Jagged backbone traces can be seen in the Vines and Thin Backbone Views. Smoothed backbone traces can be seen in N->C Rainbow (Views tab). Smoothed ribbon representations of the backbone can be seen in Secondary Structure and Cartoon (Views tab).
- Background color, black or white: The background color toggle button is the second square button in the Molecule Information Tab, Views Tab, and Tools Tab.
- Beta strands/sheets: See Secondary Structure.
- Biological unit: The common functional quaternary structure of a molecule. Also called the "biological assembly" or "specific oligomer". Further explanation, as well as an easy way to visualize the biological unit, are available in the Resources Tab, or in the Molecule Information Tab.
- Biological unit/assembly: The functional quaternary form of the molecule. Available in the Resources tab.
- Bound box: The bound box (a box parallel to the Cartesian axes that contains all atoms in the asymmetric unit) can be displayed: use Advanced/Technical in the Tools tab.
- Browser compatibility: Click on "Troubleshooting" under the molecular view, or "Trouble?" near the bottom of any tab except Preferences..
- Carboxy terminus: See N->C Rainbow.
- Cartesian coordinate axes: See Axes.
- Cartoon: In the Views tab. Each chain is given a distinct pastel color.
- Cation-pi interactions: Use Salt Bridges/Cation-Pi in the Tools tab. Protein-protein cation-pi interactions, to any protein moiety you select, are also shown by Contacts, in the Tools tab.
- Cationic amino acids: See Charge.
- Center an atom: Use the "Center Atom.." dialog available from a link near the bottom of any tab except Preferences.. It will remain centered during rotation or zooming.
- Center the entire molecule: This option is available in the "Center Atom.." dialog, which is available from a link near the bottom of any tab except Preferences..
- Chain details: The length, composition (protein, DNA or RNA), taxonomic source, and expression system are shown when you click "Chain details" in the Molecule Information Tab.
- Chain length: See Chain Details.
- Chain termini: See Ends.
- Chain, definition: See Chain in Proteopedia, which is linked to the count of chains just below "Asymmetric Unit" in the Molecule Information Tab.
- Chain, finding a specific one: Click on one of the chain names, following the count of total chains (just below "Asymmetric unit") in the Molecule Information Tab.
- Chains, total number: Given just below "Asymmetric unit" in the Molecule Information Tab.
- Charge: In the Views tab. Atoms or residues that are anionic or cationic at neutral pH are colored red and blue, respetively. The total numbers of charges in the model are reported.
- Charges on protein chain termini: Listed under Charge (Views tab) and under Ends (Tools tab).
- Chemical elements, counts, and finding in the molecular view: See Elements, Chemical.
- Citing FirstGlance in Jmol: There is no journal publication, so please simply cite http://FirstGlance.Jmol.Org
- Color scheme: Color schemes are preset in FirstGlance, not customizable. However, please see Customized views.
- Complaints to
- Composition: In the Views tab. A solid rendering in 5 colors: protein, DNA, RNA, ligand+, solvent.
- Conserved residues: Use Evolutionary Conservation in the Resources tab.
- Conformations, Alternate: See Alternate Locations.
- Contact
- Contacts & Non-Covalent Interactions: In the Tools tab. Isolates contacts to any moiety that you specify. Probably the most powerful tool in FirstGlance. Checkboxes simplify the view by showing you only one of seven categories of non-covalent interactions at a time.
- Copyright of FirstGlance: See Copyright, Licenses, Acknowledgements.
- Core, hydrophobic: Can be seen by turning on the Slab button (in the Views or Tools tabs) while coloring the molecule with Hydrophobic/polar (in the Views tab).
- Count of residues: See Number of Amino Acids and Number of Nucleotides.
- Counts of atoms: See Atom counts.
- Credits: See Copyright, Licenses, Acknowledgements.
- Cryo-EM:
- Crystal contacts: Can be visualized in one click in the Tools tab.
- Custom color scheme: See Customized views.
- Custom molecular model: If you have a customized molecular model, perhaps a homology model, you can upload it at Firstglance.Jmol.Org.
- Customized views: FirstGlance is not designed to enable you to customize the molecular view. You cannot customize the colors or rendering. This keeps FirstGlance much simpler. Easy to use tools for making customized molecular scenes are available at Proteopedia.Org. Best of all, the molecular scenes you make there are immediately available online to share with anyone.
- Cyclic nucleotides such as cyclic-AMP, cyclic-GMP, etc.
- D amino acids
- Data file contents: See PDB file contents.
- Date of deposition in the PDB.: Displayed when you touch the Date of Publication with the mouse. Also shown near the bottom of the Molecule Information Tab.
- Date of publication: In the Molecule Information Tab just below the cluster of square buttons. Also shown near the bottom of the Molecule Information Tab. Also called the "release date". This may be later than the date when the entry was deposited in the PDB. See "Date of deposition". Some journals require release on the date of publication of the journal article.
- De-clutter the view: See Simplify View.
- Delete parts of the model.: You can't actually delete the data (unless you edit the PDB data file), but you can easily hide them. See Hide.
- Deoxyribothymidine
- Different molecule: Click on "New" near the bottom of any tab except Preferences.. Or if FirstGlance is not already running, google the word firstglance (no space between First and Glance!) and FirstGlance in Jmol will be one of the top hits.
- Dihedral angles: Use Distances/Angles in the Tools tab.
- Dimensions of the model: Use Distances/Angles in the Tools tab.
- Distance between atoms: Use Distances/Angles in the Tools tab.
- Disulfide bonds: In the Tools tab. Highlights and counts disulfide bonds, as well as cysteines. Also counts sulfurs and selenium atoms, as well as methionines. Disulfide bonds are shown as thin yellow bars in the initial view, but may be difficult to see. In the Lower Left Panel help about disulfide bonds are listed many example PDB codes illustrating various cases.
- DNA: See Composition
- Dots: See Anomalous atoms.
- Educators: See Plans for teaching ... under the Resources Tab.
- Electron microscopy: See Experimental Method.
- Electrostatic density map: FirstGlance does not offer a surface colored by electrostatic density. However a similar view is obtained with Charge in the Views Tab.
- Electrostatic interactions: Use Salt Bridges/Cation-Pi in the Tools tab. See also hydrogen bonds in the Contacts and Non-Covalent Interactions Tool.
- Element, chemical, finding in the molecular view: Enter the full name of the element in the "Find.." dialog, such as selenium or zinc. Unusual elements will be listed under Ligands in the Molecule Information Tab. You can click their codes to locate all copies in the molecular view.
- Element, chemical, identifying: Click on an atom to identify it. A report including the chemical element will appear underneath the molecule.
- Elements, chemical, list: All chemical elements in the model are listed in the Molecule Information Tab, just below the atom count, under Asymmetric Unit. Clicking on the elements link reports the atom count for each element. Links by each atom count make it easy to find the atoms of a chemical element.
- Empty baskets: These can be hidden with a checkbox that will appear when you click "Missing Residues" in the Molecule Information Tab. Clicking the link "Missing Residues" also provides an explanation.
- Ending a session: Simply close the tab or window, or click on "Close" near the bottom of any tab except Preferences..
- Ends of protein or nucleic acid chains: To examine them in close detail, click Ends.. in the Tools tab.
- Erase distances and angles: A link to erase distance monitor lines and angle lines is in the Lower Left Panel after you click Distances/Angles in the Tools tab. Another one is available after you display Contacts & Non-Covalent Interactions (Tools tab): look below the postage stamp-sized snapshots for "Distances: How? Hide".
- Erase parts of the model: See Hide.
- Evolutionary conservation: Available in the Resources tab.
- Experimental method: The method used to determine the model. Shown in the Molecule Information Tab just below the cluster of square buttons. Usually X-Ray Diffraction, sometimes NMR, rarely cryo electron microscopy.
- Feedback to
- Find a component of the model: Use the "Find.." dialog available from a link near the bottom of any tab except Preferences..
- Finding a model of your molecule: Use the Practical Guide to Homology Modeling, which also tells how to find X-ray or NMR models.
- Finding a specific chain: Click on one of the chain names, following the count of total chains (just below "Asymmetric unit") in the Molecule Information Tab.
- Free R: Shown in the Molecule Information Tab as "Reliability" with a link to an explanation.
- Functional sites: Can be identified as patches of evolutionarily conserved residues. Use Evolutionary Conservation in the Resources tab.
- Gallery of molecules: Available through a link at Firstglance.Jmol.Org. See also Atlas.MolviZ.Org.
- Getting a model of your molecule: Use the Practical Guide to Homology Modeling, which also tells how to find X-ray or NMR models.
- Graphics: See Images or see Animations.
- Hide distances and angles: A link to erase distance monitor lines and angle lines is in the Lower Left Panel after you click Distances/Angles in the Tools tab. Another one is available after you display Contacts & Non-Covalent Interactions (Tools tab): look below the postage stamp-sized snapshots for "Distances: How? Hide".
- Hide parts of the model: Use the "Hide.." dialog available from a link near the bottom of any tab except Preferences.. If you want to hide all but one component, use the "Isolate.." dialog linked next to Hide.
- Hiding empty baskets: These can be hidden with a checkbox that will appear when you click "Missing Residues" in the Molecule Information Tab. Clicking the link "Missing Residues" also provides an explanation.
- Homology modeling: Use the Practical Guide to Homology Modeling, which is linked to the initial page at Firstglance.Jmol.Org, and in the Resources tab.
- How many atoms?: See Atom counts.
- How to find a model of your molecule: Please see Finding a model of your molecule.
- Hydrogen atoms: When present in the model (unusual), the percentages of protein and nucleic acid atoms that are hydrogen are given in the Molecule Information Tab. These are linked to an explanation of how to interpret these percentages. At the bottom of that explanation is a list H/non-H Atom Counts by Composition. When no hydrogen is present in the model, you will see "No hydrogen atoms" linked to an explanation.
- Hydrogen bonds: FirstGlance does not (yet) show hydrogen bonds as sticks between atoms. Rather, it isolates potential donor/acceptor pairs of atoms for putative hydrogen bonds. Ust Contacts in the Tools tab.
- Hydrophilic: See Hydrophobic.
- Hydrophobic core: Can be seen by turning on the Slab button (in the Views or Tools tabs) while coloring the molecule with Hydrophobic/polar (in the Views tab).
- Hydrophobic interactions: Shown by Contacts, in the Tools tab.
- Hydrophobic/polar: In the Views tab. Colors amino acids in two colors, according to whether their sidechains are hydrophobic or polar (hydrophilic). See also Membrane Protein.
- Identical chains: Groups of sequence-identical chains, when present, are listed under Chain Details in the Molecule Information Tab. Sequence identity is also indicated with an equal sign "=" in the list of chains in the Molecule Information Tab.
- Identify an atom: Click on an atom to identify it. A report will appear underneath the molecule.
- Image quality: See Quality.
- Images: To save an image of the current molecular view, click on "Save Image or Animation" (highlighted in orange) below the molecule. Saved images can be used in publications or presentations (Powerpoint, Google Slides, Libre Office, etc.). More information. See also: Animations.
- Incomplete models: See Missing Residues.
- Incomplete sidechains: See Sidechains, Incomplete.
- Insertion codes, when present,
- Integral membrane protein: To visualize hydrophobic surfaces of protein that may be buried in a lipid bilayer, see Hydrophobic/Polar in the Views tab. To visualize the predicted boundaries between lipid and polar environments, go to See Lipid Bilayer Boundaries in the Resources tab. Examples of membrane proteins are given in the help when you click Hydrophobic/Polar in the Views tab.
- Intrinsic disorder: Predictions are available in the Resources tab.
- Introduction to FirstGlance: The Introduction fills the Lower Left Panel at the beginning of a session. Later, you can get back to the Introduction by clicking "Return to Introduction" at the bottom of the Lower Left Panel.
- Ionic interactions: Use Salt Bridges/Cation-Pi in the Tools tab.
- Isolate a component: Use the "Isolate.." dialog available from a link near the bottom of any tab except Preferences.. If you want to isolate more than one one component, use the "Hide.." dialog linked next to Isolate, or "Find" the desired components, and then Isolate them.
- Java: Using the Jmol_S Java applet, instead of JSmol (javascript), was an option until FirstGlance version 2.7 (early 2018). The most popular browsers no longer support Java applets, and Oracle (maker of Java) plans to discontinue Java for all web browsers in the future. If you use a Java-compatible web browser, you can still use Java by adding &java to the URL: see Query parameters. See also Java and Safety.
- Journal articles: Linked below the authors in the lower portion of the Molecule Information Tab.
- Learning resources: See Plans ... under the Resources Tab.
- Length of each chain: See Chain Details.
- License for FirstGlance: See Copyright, Licenses, Acknowledgements.
- Ligands: Listed in the Molecule Information Tab. The list includes the number of each present in the model. Clicking on the code in the list marks (with yellow "halos") all copies in the molecular view. Ligands can be shown or hidden with the Ligands+ button in the Views or Tools tabs.
- Ligands+: This term includes all components of the model that are not water, and not chains of protein, DNA or RNA. For more details, click the Ligands+ button in the Views or Tools tabs. See also Ligands.
- Linking to FirstGlance: See All About FirstGlance in Jmol.
- Lipid bilayer boundaries: To visualize hydrophobic surfaces of protein that may be buried in a lipid bilayer, see Hydrophobic/Polar in the Views tab. To visualize the predicted boundaries between lipid and polar environments, go to See Lipid Bilayer Boundaries in the Resources tab. Examples of membrane proteins are given in the help when you click Hydrophobic/Polar in the Views tab.
- Literature citations: Linked below the authors in the lower portion of the Molecule Information Tab.
- Local Uncertainty: In the Views tab. Colors atoms by B factor/temperature value using either an absolute or relative color scheme. The average temperature for each chain is reported, with the lowest values for sequence-identical chains in boldface. Average temperatures for water and ligands+ are also reported. The temperature/B factor value for each atom is reported in the pop-up elicited by touching an atom.
- Locate a component of the model: Use the "Find.." dialog available from a link near the bottom of any tab except Preferences..
- Locations/Atom and Locations, Alternate: See Alternate Locations.
- Magnification: See Zoom.
- Mark a component of the model: Use the "Find.." dialog available from a link near the bottom of any tab except Preferences..
- Membrane protein: To visualize hydrophobic surfaces of protein that may be buried in a lipid bilayer, see Hydrophobic/Polar in the Views tab. To visualize the predicted boundaries between lipid and polar environments, go to See Lipid Bilayer Boundaries in the Resources tab. Examples of membrane proteins are given in the help when you click Hydrophobic/Polar in the Views tab.
- Metal interactions: Shown by Contacts, in the Tools tab.
- Method, experimental: See Experimental Method.
- Missing residues: A count of missing residues is given in the Molecule Information Tab. Clicking on "Missing Residues" there provides details for each chain, as well as an explanation. In the less common case in which all residues are present in the model, you will see "No residues missing", also linked to an explanation. This information is also summarized in the first paragraph of the Introduction.
- Missing sidechain atoms: See Sidechains, Incomplete.
- Molecular model: All published empirically-determined macromolecular models are available from the Protein Data Bank. They can also be found, when available, under the Structure section at UniProt.Org. See also Custom molecular model and Online molecular model.
- Molecule Information Tab: This tab is labeled with the PDB code unless the model is not an entry in the Protein Data Bank, or has been modified.
- Molecule's name: See Name of Molecule.
- Movies: See Animations.
- N->C Rainbow: In the Views tab. Amino & 5' termini are colored blue, carboxy and 3' termini red, with a rainbow/spectral color sequence in between.
- Name of molecule: Usually at the top of the Molecule Information Tab.
- Nature: See Adoptions.
- Negative charges: See Charge.
- Negative or zero sequence numbers
- New session: Click on "New" near the bottom of any tab except Preferences.. Or if FirstGlance is not already running, google the word firstglance (no space between First and Glance!) and FirstGlance in Jmol will be one of the top hits.
- NMR: See Experimental Method.
- Non-covalent interactions: See Contacts.
- Non-standard residues: Listed in the Molecule Information Tab. The list includes the number of each present in the model. Clicking on the code in the list marks (with yellow "halos") all copies in the molecular view. Each non-standard residue is labeled with an X in the initial view. These labels can be hidden by unchecking the Labels Show checkbox, near the bottom of any tab except Preferences.. See Labels X, S-, ?. Non-standard residues can optionally be rendered as balls and sticks: use Advanced/Technical in the Tools tab.
- Nucleoside or nucleotide, as single ligand (not part of a polymer), such as AMP, ADP, ATP, GTP, etc.
- Nucleotide, locating in the molecular view: See Find.
- Nucleotides, total number: Given as a count of pentose C5' atoms in the Molecule Information Tab. Because the 5' end of nucleic acid chains lacks a phosphorus, a count of nucleic acid phosphorus atoms would be an underestimate.
- Number of amino acids, total: Given as a count of alpha carbon atoms in the Molecule Information Tab.
- Number of nucleotides, total: Given as a count of pentose C5' atoms in the Molecule Information Tab. Because the 5' end of nucleic acid chains lacks a phosphorus, a count of nucleic acid phosphorus atoms would be an underestimate.
- Number of residues, total: See Number of Amino Acids and Number of Nucleotides.
- Obtaining a model of your molecule: Use the Practical Guide to Homology Modeling, which also tells how to find X-ray or NMR models.
- OCA browser: Available through the Resources tab. Also available for Sequences, in the Molecule Information Tab
- Occupancies: Atoms may be assigned occupancies of 100% down to 0%. The range of occupancy values is summarized in the Molecule Information Tab. Clicking on Occupancy there will produce a table listing all occupancy values and the numbers of atom locations for each, with the option to Find all instances of a given occupancy value. For an example, explore 1sjv. See also Alternate Locations.
- Oligomeric state: Use Biological Unit in the Resources tab.
- Online molecular model: Any molecular model available online can be displayed in FirstGlance. See the "molecule URL" link at Firstglance.Jmol.Org.
- PDB file contents: Can be displayed with the link "View PDB File" in the lower portion of the Molecule Information Tab.
- Percentage sign as in %A, %B, etc. Please see "%A" at the top of the A's on this page.
- Pictures: See Images.
- Plans for teaching and learning: See Plans ... under the Resources Tab.
- Polar/hydrophobic: See Hydrophobic.
- Positive charges: See Charge.
- Powerpoint presentations: See Presenting Molecular Views and Animations.
- Preferences: Use the Preferences tab.
- Presentations: See Presenting Molecular Views and Animations.
- Problems? Please contact
- Professors: See Plans for teaching ... under the Resources Tab.
- Protein: See Composition
- Protein Data Bank: Available through the Resources tab.
- Publication date: See Date.
- Publication quality image: See Quality.
- Publications: Linked below the authors in the lower portion of the Molecule Information Tab.
- Quality of the image: The quality of the molecular image can be high or normal. High quality smooths some jagged edges, but slows rotation. Toggled by a square Quality button in the cluster of buttons in the Molecule Information Tab, Views Tab, and Tools Tab.
- Quality of the molecular model: See Quality Assessment for Molecular Models, and Resolution and Free R in this index. See also Atomic Clashes in the Resources tab.
- Query parameters: See Advanced Options/Query Parameters. This document is linked in All About FirstGlance in Jmol under How to show a molecule from your website at the link How to specify a PDB identification code in a hyperlink to FirstGlance.
- Quitting a session: Simply close the tab or window, or click on "Close" near the bottom of any tab except Preferences..
- R free: Shown in the Molecule Information Tab as "Reliability" with a link to an explanation.
- R value: Shown in the Molecule Information Tab
- References for the structure: Linked below the authors in the lower portion of the Molecule Information Tab.
- Referencing FirstGlance: Please see Citing FirstGlance.
- Release date: See Date.
- Remove distances and angles: A link to erase distance monitor lines and angle lines is in the Lower Left Panel after you click Distances/Angles in the Tools tab. Another one is available after you display Contacts & Non-Covalent Interactions (Tools tab): look below the postage stamp-sized snapshots for "Distances: How? Hide".
- Report feedback to
- Reset: You can return to the initial molecular view by clicking the "Reset" link near the bottom of any tab (except Preferences).
  To reset a ConSurf result:
  If you are in ConSurf View (stated at the upper left), click the button Reset View.
  If you are in the FirstGlance controls (tabs at the upper left), click on ConSurf Controls (middle left), and after you get the ConSurf View (stated at the upper left), click on the button Reset View.
- Residue, locating in the molecular view: See Find.
- Residues, total number: See Number of Amino Acids and Number of Nucleotides.
- Resolution: Shown in the Molecule Information Tab with a link to an explanation.
- Ribbons: See Cartoon.
- Ribothymidine
- RNA: See Composition
- Rotate the molecule: Drag the molecule with your mouse
- S- labeling some residues: See Sidechains, Missing.
- Salt bridges: Use Salt Bridges/Cation-Pi in the Tools tab. Protein-protein salt bridges to any protein moiety you select are also shown by Contacts, in the Tools tab.
- Search for a component of the model: Use the "Find.." dialog available from a link near the bottom of any tab except Preferences..
- Secondary structure: In the Views tab. It reports percentages of each secondary structure.
- Sequence number, locating in the molecular view: Enter the number in the "Find.." dialog. You can also enter a range of sequence numbers, such as 22-34. See the help displayed in the "Find.." dialog for more options.
- Sequence numbers, displaying: The Sequence Numbers checkbox (any tab except Preferences.) labels every visible alpha carbon and nucleotide C5' with the sequence number.
- Sequence-identical chains: See Identical Chains.
- Sequence, locating in the molecular view: Enter a short sequence in the "Find.." dialog, as explained there. Note that you must prefix the sequence with "sequence=", for example, sequence=TRFVIM or sequence=CGGAT.
- Sequences of each chain: Click on "Sequences" in the Molecule Information Tab. Links will be shown to both the experimental (crystallized) sequence, and the full-length genomic sequence.

- New default "Shiny" rendering. | Older rendering, now a preference option.

  Shiny rendering is the default beginning with FirstGlance Version 2.85. The earlier rendering was less shiny and slightly brigheter. You can choose it under the Preferences Tab.
- Sidechains, incomplete: When some sidechain atoms are missing, this is reported in the Molecule Information Tab, and summarized in the first paragraph of the Introduction. Also, each residue with missing sidechain atoms is labeled S- in the molecular view. These S- labels can be turned off. See the checkbox for "Labels, Show" near the bottom of any tab except Preferences..
- Simplify view: You can simplfy a view by using Hide (bottom of any tab except Preferences.) to hide some portions of the model, or Isolate (bottom of any tab except Preferences.) to hide everything except one entity in a single click. Or you can use Find (bottom of any tab except Preferences.) to find a group of items, and then Isolate them (Isolate Atoms with Halos). You can also use Center Atom (bottom of any tab except Preferences.) on the are of interest, and then turn on the Slab button (Views or Tools tab). The Thin Backbone View is a simplifying view. In the Contacts Tool, you can use checkboxes to hide all but one category of non-covalent bonds.
- Size of the molecular image: The molecular image will resize when you resize the browser window. See also Zoom.
- Slab: Toggled by a Slab button in the Views and Tools tabs. Hides the front and back of the molecule, making it easier to see details of the centered portion of the model. Slab thickness can be controlled with radio buttons. A checkbox keeps the back of the molecule visible, which is useful for seeing the insides of cavities and channels.
- Snapshots of the molecule: See Images.
- Solid view: In the Views tab. All atoms are rendered at van der Waals radii. Other solid views are Composition, Hydrophobic/Polar, and Charge (all in the Views tab).
- Source (taxonomic) of each chain: See Chain Details.
- Species for each chain: See Chain Details.
- Specifications: See Troubleshooting.
- Spin toggle button: The first square button in the Molecule Information Tab, Views Tab, and Tools Tab. Whether the molecule spins initially is a setting in the Preferences tab.
- Start over: You can return to the initial molecular view by clicking the "Reset" link near the bottom of #NOPREFS
- Starting a new session: Click on "New" near the bottom of any tab except Preferences.. Or if FirstGlance is not already running, google the word firstglance (no space between First and Glance!) and FirstGlance in Jmol will be one of the top hits.
- Sticks: See Vines/Sticks.
- Students, Study: See Plans for learning ... under the Resources Tab.
- Summary of the publication: Available with an "Abstract" link in the lower portion of the Molecule Information Tab.
- Syllabi for teaching and learning: See Plans ... under the Resources Tab.
- Taxonomic source of each chain: See Chain Details.
- Teaching plans for educators: See Plans ... under the Resources Tab.
- Technical information: See the bottom section in the Notes for FirstGlance.
- Temperature factor: See Local Uncertainty.
- Termini of chains: See Ends.
- Thickness of the model: Use Distances/Angles in the Tools tab.
- Torsion angles: Use Distances/Angles in the Tools tab.
- Total atoms in model: See Atom counts.
- Transmembrane protein: To visualize hydrophobic surfaces of protein that may be buried in a lipid bilayer, see Hydrophobic/Polar in the Views tab. To visualize the predicted boundaries between lipid and polar environments, go to See Lipid Bilayer Boundaries in the Resources tab. Examples of membrane proteins are given in the help when you click Hydrophobic/Polar in the Views tab.
- Troubleshooting: Click on "Troubleshooting" under the molecular view, or "Trouble?" near the bottom of any tab except Preferences..
- Troubleshooting: See Troubleshooting.
- Un-clutter the view: See Simplify View.
- Undo: Regrettably, there is no general "Undo" capability. Some dialogs (Hide, Isolate, Find) have undo capabilities. If you want to go back to the initial molecular view, click the "Reset" link near the bottom of any tab except Preferences..
- Unfolded regions: Predictions of intrinsic disorder are available in the Resources tab.
- Unit cell: Can be visualized in one click in the Tools tab.
- Unknown atoms "X", groups "UNX" or "UNK", nucleotides "N", or ligands "UNL"
- Unusual components or features are alerted when the molecule is first loaded. See this list.
- van der Waals interactions: Shown by Contacts, in the Tools tab.
- Version history: See Version History, or click on the version number shown below the molecule.
- Videos, saving: See Animations.
- Vines/Sticks: In the Views tab. This view shows all non-water atoms as bond-sticks (wireframe rendering). Main chain atoms are simplified to a backbone trace initially, with sidechains shown as sticks (like leaves on a vine). All atoms (including main chain atoms) can be shown when more detail is checked. Atoms not covalently bonded to other atoms (such as water oxygens) will be tiny isolated spheres.
- Water: Turning on the Water button (Views or Tools tabs) reports the number of water molecule present in the model, and displays any present at van der Waals radii. A checkbox in the Lower Left Panel of help for Water renders the water molecules as smaller spheres.
- Water bridges: Can be isolated and visualized with Contacts, in the Tools tab.
- What chain is this?: Each chain has a one-character "name". Click on any atom in a chain, and its chain name will be reported beneath the molecule. Or you can simply touch an atom in the chain and a tooltip will appear identifying the atom and chain.
- What is FirstGlance in Jmol?: See What Is FirstGlance in Jmol?.
- What residue is this?: Click on any atom in the residue of interest. A report will appear beneath the molecule that identifies the residue and atom that you clicked. Or you can simply touch an atom and a tooltip will appear with its identification.
- Wireframe: See Vines/Sticks.
- X-ray crystallography: See Experimental Method.
- Zero or negative sequence numbers
- Zoom: See the clickable black arrows in the cluster of buttons in the Molecule Information Tab, Views Tab, and Tools Tab. Clicking one of these arrows provides other methods for zooming. See also Size.

End of Index