• 1 covalent N-linked glycosylation.
• 1 covalent peptide bond to residue 249.
• 23 hydrogen bonds: chain D to upstream chain D residues and to chain B, plus chain D to glycosylation.
• 61 apolar carbon-carbon interactions.
• 14 protein-protein salt bridges between chain D and chain B.
• 2 cation-pi interactions between chain D and chain B, each of which involves 12 atom pairs.

1. Load 1igt.
2. Click the Tools tab at the upper left.
3. Click Find.. (in the Focus Box).
4. Type 250-474 and chain=D in the Find slot and press Enter.
5. Click Contacts & Non-Covalent Interactions near the upper left.
6. Check Atoms with Halos.
7. Click Show Atoms Contacting Target.
8. Scroll down in the lower left panel until you see List Contacting Atoms & Bonds, and click that.

1. Load 1HXW.
2. Click Find.. (in the Focus Box).
3. Type helix into the Find slot, and press Enter.
4. Click on the pink-highlighted List Found Atoms.
5. In the Find slot, change helix to helix and calpha.
6. Click on the pink-highlighted List Found Atoms.
7. Go to the Views tab, and click the Ligands+ button once or twice, leaving it depressed.
8. Below the Ligands+ color key, click on Find ~ligandsPlus.
9. Click on the pink-highlighted List Found Atoms.

1. Load 1vao pre-processed by ConSurf
2. Click Go to the FirstGlance Control Panel (top left).
3. Click the Tools tab at the top left.
4. Click Contacts & Non-Covalent Interactions
5. Click on chain A (light blue) to designate it as the target.
6. Cancel treating as part of the target the ligands+ associated with chain A. This means that the interactions between amino acids in chain A and its FAD and acetate (ACT) ligands will be displayed and listed. (If you click OK, they will not be. After completing this procedure, you could go back to step 4 to compare the other option.)
7. Check Target Water within Target Chain(s) This avoids cluttering the result with all the hydrogen bonds between chain A and its associated water. Hydrogen bonds between chain A and water not associated with chain A will still be displayed and listed.
8. Click Show Atoms Contacting Target. The result is complex; visual analysis would be time consuming. Listing the contacts may be more useful:
9. Scroll down in the lower left panel to find the yellow button List Contacting Atoms & Bonds and click it. The report is generated in a new browser tab.

Alternate locations of sidechains were previously handled well, and could be animated. However, in schematic backbone trace views (cartoon, secondary structure, N->C Rainbow, vines/sticks, thin backbone), backbone forks were not visible, and animations did not work for backbone forks. (Technical: This was because of the belated realization that the JSmol commands "select all;cartoon;" render only conformation 1 as cartoon, leaving conformation 2 invisible. Subsequently issuing the command "conformation 2;" renders conformation 2 as cartoon, but hides conformation 1. It is apparently not possible to show both conformations as cartoon simultaneously from a single model.)

The Alternate Locations Server kindly implemented by Jaime Prilusky has been indispensable. Tremendous thanks to Bob Hanson for enhancements to Jmol, and consulting on alternate locations, conformations, and Jmol command code.

Animation of the 3 conformations of 5sop: 1 2 3. Common to all conformations. Pink = Singletons. Secondary Structure View (without rockets) colored by conformations. This is a major oversimplification of all possible conformations. Instructions for capturing such videos/GIFs.

• The Contents of How to Use FirstGlance has been reorganized and expanded.
• YouTube video demonstrating detection and analysis of protein crosslinks.
• ConSurf: an new overview of using the ConSurf Server for visualizing and listing conservation levels of amino acids, and how PDB-files pre-processed by ConSurf interface with FirstGlance.
• How FirstGlance Counts Amino Acids.
• How FirstGlance Counts Nucleotides.
• About Alternate Locations:
  • Alternate locations, conformations & backbone forks.
  • How FirstGlance defines conformations.
  • Alternate Locations vs. Singletons and Occupancies in PDB Files.
  • Find.. and alternate locations.
  • Isolating Atoms With Alternate Locations.
  • How to use the Contacts & Non-Covalent Interactions Tool with alternate locations.
  • Salt Bridges vs. Alternate Locations.
  • Cation-Pi Interactions vs. Alternate Locations.

By default, FirstGlance starts in "fewer details mode". Clicking Show More Details checks "Alert for unusual components or features" in the Preferences tab.

• 1ntp: Deuterium in protein (no water in this model).
• 3qba: Deuterium in DNA and water (DOD).
• 7ucr: Deuterium in RNA and water (DOD).

• EXAMPLES of the following cases are available in a new explanation about Counting Amino Acids.
• Most cases having a mixture of some amino acids modeled as alpha carbons only, and others modeled as main chain atoms only, or complete amino acids, will be reported correctly.
• When showing more details, standard amino acids that have at least a beta-carbon, but are missing other sidechain atoms, are reported as having incomplete sidechains.
• Detection of incomplete sidechains is expanded to include the rare 21st and 22nd standard amino acids, selenocysteine (Sec, U), and pyrrolysine (Pyl, O).
• Fragmentary amino acids lacking main chain alpha carbons, nitrogens, carboxy carbons, or main chain oxygens are reported.
• The count of unknown amino acids designated "UNK" is newly reported (in addition to an alert).

• EXAMPLES of the following cases are available in a new explanation about Counting Nucleotides.
• In addition to the count of C5' atoms, the count of phosphorus atoms is now reported when it exceeds the count of C5' atoms.
• Most cases having a mixture of some nucleotides modeled as phosphorus-only, and others modeled as phosphate only, phosphoribose or complete nucleotides, will be reported correctly.
• Standard nucleotides that have any base atoms, but are missing some base atoms, are reported as having "incomplete bases".
• Newly documented are Unknown nucleic residues "N", and their count is newly reported. Examples.

• 1usi has a monomeric Phe amino acid ligand.
• 1g2v has 8 monomeric deoxy thymidine triphosphate (TTP) ligands.

• 1igt: Antibody with glycosylated heavy chains.
• 1jyn: Beta-galactosidase with bound lactose.

• 4FFL
• 1g2v
• 1usi

• 2 chains: ConSurf-preprocessed 4ENL. (For 2-3 chains, there are checkboxes for each chain.)
• 4 chains: ConSurf-preprocessed 1flo. (For ≥4 chains, there is one checkbox for all chains.)
  (Technical note: see #13x in make_for_spt() in consurf/main_cs.js, and #13y/z in help_cs.js.)

The design error caused multiple problems. The initial display of uploaded ConSurf files was the asymmetric unit, but should have been biological unit 1. When biological unit 1 was smaller than the asymmetric unit, displaying biological unit 1 caused "solid" atoms to be too large, and erroneously reported that the model contained only alpha carbons. This error precluded use of the Vines/Sticks View, and most Tools.

• Compare handling of 4b14_consurf.pdb vs data1.pdb. Asymmetric unit has 3 chains. Each biological unit has 1 chain.

• Biological Unit 5 for 1zw0 with Chain D processed by ConSurf. Of less importance, with chain D processed by ConSurf, the chain to which ConSurf colors are initially applied was often not D (though sequence-identical to D), despite D being present.
• Biological Unit 15 for 1zw0 with Chain D processed by ConSurf. Chain D is absent, but chain D1 is present and colored initially.
• Biological Unit 5 for 6nca with chain A processed by ConSurf. In Biological Unit 5, chain A is absent, so sequence-identical chain T is colored initially.
• Biological Unit 1 for 1ucy with chain K processed by ConSurf. Neither chain K nor any chain sequence-identical with K is present in Biological Unit 1. FirstGlance automatically reverts to the asymmetric unit, which contains all chains present in any biological unit, and explains the situation. Biological Unit 2 includes chain K. Biological Unit 3 lacks chain K, but has chain N which is identical in sequence.

• A minimal header section enables functional assemblies (REMARK 350) to be interpreted: conservation.pdb.
• No header section (not an AlphaFold prediction): conservation-noheader.pdb.

1. For biological assemblies in which chains in the asymmetric unit are duplicated: Each asymmetric unit chain and its duplicates get a single distinct color.
2. Each group of sequence-identical chains gets a distinct color. A good example illustrating the differences between this and the previous color scheme is 1ej6. Further examples.
3. Secondary structure.
4. N->C Rainbow.
5. Distance from the center of the structure in spectral colors.
6. Distance from the center of the structure in grayscale. This emphasizes the depths of valleys in a surface.

Reovirus Core 1ej6. 300 chains: 60 duplicates of the 5 chains in the asymmetric unit. Simplified to every 11th alpha carbon. Diameter ~725 Å.
1. Five Duplicated Chains	2. Three Distinct Sequences	5. Color by Distance	6. Grayscale by Distance

ConSurf PDB Files are Special Cases: Evolutionary conservation of amino acids in unpublished PDB files can be determined by uploading the PDB files to the ConSurf Server. ConSurf prepares a downloadable PDB file customized for FirstGlance, containing the conservation results. These ConSurf PDB files are handled by FirstGlance as special cases: the initial view will be Biological Unit 1 (instead of the asymmetric unit as is the case for other .pdb files), automatically simplified as needed. See examples, including important instructions for unpublished ConSurf PDB files.

• 1abc is an unassigned PDB code.
• 2cx2 was withdrawn by its depositors before being released.
• 1vsz is an obsolete PDB code, superseded by a newer code.
• Entries being held for publication. In June, 2022, 8d86 had status HPUB, and 7v0r had status HOLD. You can search for entries currently being held at rcsb.org/pages/unreleased.

This requires FirstGlance version 3.8 or later, which may not yet be installed on the ConSurf Server. Therefore, at the ConSurf Server, you should download the PDB file for FirstGlance, and then upload it to the latest FirstGlance.Jmol.Org.

• Are now displayed in accordance with the ConSurf Colors checkbox.
• The ConSurf color key obeys the color scheme encoded in the ConSurf PDB file. For example, the user may choose a "color blind friendly" color scheme instead of the default (try 2VAA with ConSurf Color Blind Scheme).
• When chains not sequence-identical to the chain processed by ConSurf are present (try the 2VAA example above), their color key will also be displayed.

• AlphaFold Colab prediction with no header section: Secreted in Xylem 1 of Fusarium oxysporum (Q709E2). You will be asked whether this is an AlphaFold prediction.
• AlphaFold Database prediction with header section: Iron phytosiderophore transporter of Zea Mays (Q9AY27). FirstGlance automatically determines that this is an AlphaFold prediction.
• AlphaFold Colab prediction processed with ConSurf: Secreted in Xylem 1 of Fusarium oxysporum (Q709E2). You will be asked whether this is an AlphaFold prediction. Includes putative ester crosslink (actually a clash).
• AlphaFold Database prediction processed with ConSurf: Iron phytosiderophore transporter of Zea Mays (Q9AY27). FirstGlance automatically determines that this is an AlphaFold prediction.

• RoseTTAFold prediction for a Fusarium oxysporum protein of unknown function: RoseTTaFold prediction for UniProt W9JUF2.
• ConSurf analysis of the above RoseTTAFold prediction.

• Alerts for unusual components or features. (The previously existing preference for these alerts is turned off.) Example: 6cty. If you toggle from fewer to more details, these alerts will be shown.
• Molecular Views:
  • Atoms with alternate locations. Simple example: 3hyd.
• Hide Dialog (in the Focus Box):
  • Alternate locations checkbox.
  • When hiding is inverted, the automatically-hidden alternate locations remain hidden.
• Molecule Information Tab:
  • The R value. (Free R and its interpretation remain visible.)
  • Count of non-glycines lacking beta carbons. Example: 1ijw.
  • Count of incomplete sidechains. Example: 1ijw. (S- labels and count in Introduction remain visible.)
  • Count of putative isopeptide bonds. Example: 3htl.
  • Count of putative cysteine thioester protein crosslinks. Example: 2xi9.
  • Count of putative cysteine thioether protein crosslinks. Example: 6e87.
  • Count of putative threonine (or serine?) ester protein crosslinks. Example: 4mkm.
  • Count of putative histidine-tyrosine protein crosslinks. Example: 1v54.
  • Count of possible Lys-Cys NOS bonds. Example: 6zx4.
  • Alternate locations. Simple example: 3hyd.
  • Occupancies. Example: 1ijw.
  • Link to view the PDB file.
  • Deposition date.
  • Related PDB entries. (New in this version.) Example: 1ijw.
• Introduction:
  • Count of alternate locations.
• Views Tab:
  • The Local Uncertainty color scheme.
• Tools Tab:
  • Crystal contacts tool.
  • Unit cell tool.
  • Advanced/Technical.
• Alternate location, occupancy, and temperature (B factor) when you touch (hover over) or click an atom.

• In the Find.. dialog (Focus Box) after specified atoms have been identified with yellow halos.
• In the Ends.. dialog (Molecule Information tab/Tools tab) after one end of a chain has been displayed.
• For Protein Crosslinks (Tools tab), after one crosslink has been displayed.

• Extensive introductions and explanations are linked.
• FirstGlance determines whether the map is available before attempting to display it. Example: the map data for 1d66 were not deposited in the PDB. The PDB began requiring deposition of maps with models in 2008.
• The map isomesh can be shown within 3 or 5 Å of the target atoms.
• For X-ray models, the electron density map can be displayed for all features (2Fo-Fc), or for differences between the map and the atomic model (Fo-Fc).
• The target atoms are shown as sticks within the map. A checkbox displays them as balls and sticks.
• Controls are offered for slab thickness.
• The target atoms are colored by chemical element, with options to color them by absolute or relative temperature/B factor.
• Static images or presentation-ready animations (example at right) can be saved. See examples of static images for all-features and difference maps at Electron Density Maps in Proteopedia. More animations are in the slides that illustrate various animations saved from FirstGlance: tinyurl.com/movingmolecules.

• 5XAA has N-terminal acetylation (1 line).
• 3ZZZ has an N-terminal expression tag (missing; 6 lines).
• 4a00 has engineered mutations (3 lines).
• 3odL has engineered modifications of a non-standard residue (10 lines).
• 4adp has expression tags at both ends (both ends missing), and one engineered mutation with different sequence numbering in the model vs. UniProt (10 lines).
• 1zeL has cloning artifacts and a conflict (8 lines).
• 2e00 has an N-terminal expression tag (with coordinates), one engineered mutation, and one deletion (6 lines).
• 1CGQ has insertions (3 lines).
• 110L has sequence conflicts (3 lines).
• 2f0w has 4 engineered mutations and one variant (5 lines).
• 2dxd referenced a non-existent REMARK 999, but when reported to the wwPDB it was remediated. Now its SEQADV lists initiating methionines and expression tags (all missing coordinates; 6 lines).
• 2ffi has modified residues (Met to MSE = selenomethionine), cloning artifacts, and a C-terminal expression tag (mostly missing; 30 lines).
• 6pv7 has linkers, conflicts, and C-terminal expression tags (missing coordinates; 45 lines).

• 1v00: chirality errors even with resolution 1.7 Å and Rfree better than average.
• 1aaQ: atomic clashes.
• 5uu5: improper peptide linkages.
• 5a0a: "long bond".

• D-amino acids are labeled "D", instead of the "X" used for other non-standard residues.
• The count of D-amino acids, and their percentage of non-Gly amino acids are reported in the Molecule Information Tab. The count of D-amino acids is also alerted at the outset as unusual components.
• Incomplete sidechains in D-amino acids are now marked S- and reported in the Molecule Information Tab. ("S-" supersedes "D"). Example: 5e5t.
• Charge (Views tab) now colors and counts D-amino acid charges correctly. Examples are given in the lower left (help) panel.
• Disulfides/S/Se (Tools tab) now handles Dcy-Dcy and Cys-Dcy disulfide bonds correctly. Examples are given in the lower left (help) panel.
• Salt Bridges/Cation Pi (Tools tab) now reports salt bridges involving charged sidechains of D-amino acids. Examples are given in the lower left (help) panel.

                              Asymmetric  Biological
 Code   Method                  Unit?       Units*
•1d66:  X-ray Diffraction        Yes          0
•1hho:  X-ray Diffraction        Yes          1
•1b6b:  X-ray Diffraction        Yes          2 (monomers)
•5cev:  X-ray Diffraction        Yes          2 (hexamers, neither = asymmetric unit)
•1qrd:  X-ray Diffraction        Yes          2 (software determined more likely than author determined)

•5mny:  Neutron Diffraction      Yes          0
•2yz4:  Neutron Diffraction      Yes          1

•6pkj:  Electron Crystallography Yes          0
•6oiz:  Electron Crystallography Yes          1

•2bbn:  Solution NMR             No           0†

•5v7z:  Solid State NMR          ?            0
•2c0x:  Solid State NMR          ?            1

•6ef8:  Electron Microscopy      No           0
•6nef:  Electron Microscopy      Yes          1

*Not counting the asymmetric unit, which is sometimes designated as a biological unit.
† A search of the PDB finds no solution NMR entries with biological unit assembly operations (Sept. 14, 2019).

• Are now included in Ligands+ and in the initial view are rendered solid (spacefilling atoms). Previously, they were rendered as a tiny fragment of cartoon "coil", difficult to see, especially since they had the same chain ID and color as the chain to which the dipeptide is bound. In fact, the PDB considers dipeptides to be ligands: see policy and explanation which lists some examples.
• Also, now you will be alerted to the presence of dipeptides as unusual components.
• Also, amino acids listed under Ligands+ and Non-Standard Residues (Molecule Information Tab), when in dipepides, have a link to put halos on dipeptides.

• Secondary structure determination by JSmol. You can view the author-specified secondary structure immediately, but if you ask to view JSmol's objective secondary structure, there will be a small delay while the calculation is performed.
• Characterization of chain termini, needed for the Ends View. Locating the ends of chains and determining whether the terminal charges are missing is not trivial.
• Preparation for viewing charges. This includes characterization of chain termini and whether the charged terminal residues are missing or the terminal charges are blocked.

• 6hww (biological unit) has 3,528 incomplete sidechains, which are 89% of its 3,978 amino acids.
• 5x50 has 790 incomplete sidechains, which are 21% of its 3,829 amino acids.
• 5x9z has 3,099 incomplete sidechains for 91% of its 3,418 amino acids.
• 2ace, in contrast, has 23 incomplete sidechains, 4% of its 527 amino acids.

• Now reports 3₁₀ and pi helices as well as alpha helices.
• The default display now uses secondary structure calculated by JSmol. Alternatively, radio buttons offer to show the authors' designations.
• When portions of the protein are hidden, percentages of each secondary structure element are now reported for only the visible protein. (Previously, the percentages were always for the entire model.)

• Caffeine.
• Links using FirstGlance at Metal-Ligand Polyhedra (in Proteopedia).

• When the PDB file lacked a header, this option was reporting "undefined" for water and non-water solvent.
• The count given for "non-H for ligand" included hydrogen.

• Download FirstGlance animations in Powerpoint.
• View FirstGlance animations in Google Slides.

• When the model includes selenium (Se), you are referred to Disulfides/S/Se in the Tools tab.
• When the model includes selenomethionine (MSE), a link is provided to an explanation. Example: 4hik.

• Spoof Chrome*
• Spoof Edge
• Spoof Firefox
• Spoof Internet Explorer
• Spoof Maxthon (JSmol recommendations are more urgent in Windows)*
• Spoof Opera*
• Spoof Safari

• Spoof Internet Explorer
• Spoof Edge
• Spoof Opera
• Spoof Firefox

• Spinning when the session begins is now optional.
• When using JSmol, you can hide the suggestions for browsers that perform better. Exceptions:
  • Because the performance of Internet Explorer with JSmol is unacceptably slow, the suggestion not to use it cannot be hidden.
  • Because rotation in Opera is unacceptably slow/jerky, the suggestion not to use it cannot be hidden.
• When using JSmol, you can hide the recommendation to use Java for better performance.

• Spoof Internet Explorer
• Spoof Opera
• Spoof Firefox

1. Name of the molecule.
2. Dates of deposition and release.
3. Method of structure determination.
4. Resolution, R value and free R. Resolution and free R are graded by FirstGlance to help novices interpret these values.
5. Asymmetric unit:
   1. The number of chains, and the number of sequence-distinct chains. Clickable chain names identify the location of each chain.
   2. Details about each chain including its length, whether protein, DNA or RNA, presence of non-standard residues.
   3. Sequences are easily accessible from links to various sequence databases. (There is still no clickable sequence-to-structure listing -- it remains under development.)
   4. The total number of missing residues. Also a summary table listing the residues missing in each chain, and their sequence numbers, and the number of charged residues that are missing. (The S2C "gaps" server is no longer necessary.)
6. The biological unit is readily accessible.
7. Ligands and non-standard residues are listed with their counts and full names. Clicking on one shows its position(s) in the model.
8. The publication abstract at PubMed is one click away.
9. All literature citations given in the PDB file are listed, with clickable PubMed ID and DOI links.
10. The PDB file text is one click away.

1. The Find.. tool now finds amino acid or nucleotide sequence fragments, e.g. sequence=skek or sequence=cgg.
2. The Hide.. tool now asks whether you wish to hide all copies of the residue/group or atom you clicked, or only the single one clicked.

• In the Hide.. tool, with the range option, formerly when the higher sequence number was clicked first, hiding failed.
• In the Hide.. tool, with the Atom option, the red list of atoms hidden inadvertantly included the XYZ coordinates of the atom (evidently due to a change in Jmol). Also clicking the same atom twice (possible even after it is "hidden" in some displays) was not properly handled.
• In the Find.. tool, there were problems when the query included a single quote, as in *.c5'.
• The Backbones checkbox in Contacts Shown was not being remembered.

• FirstGlance now uses Jmol.js for the first time.
• The division layout (file fg.htm) was restructured following the resizable Jmol scheme kindly provided by Angel Herráez.

• Support for ConSurf increased the size of FirstGlance by about 25% (from 15K lines in .htm and .js files to 20K). Most of the code was adapted from Protein Explorer. More..
• This involved the first use of messageCallback from Jmol to javascript, which enabled the following change, and will enable future enhancements.

1. Hide sidechains.
2. Display more detail: all non-water atoms as sticks,
3. Hide hydrogen.

• Turning centering off after a single centering click was not possible, because in "set picking center" mode, Jmol 10.00.46 does not call pickCallback(). Using "center atomno=" instead of "set picking" could have avoided this, but it caused unwanted changes in zoom.
• The present implementation was complicated by the need to turn centering off automatically, when some view links or buttons are pressed by the user before centering was turned off. This was implemented.