• S- marks incomplete Sidechains*. Find: ~incomplete_sidechain_residues
• X marks non-standard residues (other than D-amino acids). Find: ~nonstandard_residues and not ~d_aas
• D marks D-amino acids. Find: ~d_aas
• ? marks anomalous atoms. Find: ~anomalous_atoms

• 6hww has 588 incomplete sidechains, which are 89% of its 663 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.

• Structure: After you put halos on something with Find, you can apply Isolate to "Atoms with halos". Then, view as Vines/Sticks and check "More detail". At right: Ala-Pro dipeptide in 2cyh.
• Contacts: After you have halos on something, click Contacts & Non-Covalent Interactions in the Tools tab, and target Atoms With Halos.

• Subset 1 is selected with not (protein,nucleic,water), where protein is defined as Jmol's term "protein", plus the 20 standard amino acids. (Earlier versions of Jmol occasionally failed to identify some amino acids as protein.) [More..]
  
  This subset includes substrate or inhibitors, prosthetic groups such as heme, cofactors such as NAD, carbohydrate, metal ions, and so forth, regardless of whether these are covalently or non-covalently bound to the protein or nucleic acid chains. Examples are cadmium in 1D66, heme (HEM) in 2HHD, glycosylation of the protein in 1IGT, and detergent (OCT) and phosphorylation of serine and threonine (SEP and TPO) in 1APM.
  
  
• Subset 2 includes standard amino acids or nucleotides that are not part of a polymer chain (isolated single residues, single residue "chains") or that lack certain standard atoms. If not included in Ligands+, these would be invisible in displays such as Cartoon, Secondary Structure, N->C Rainbow, and Vines with sidechains hidden. Examples include GLY308 in 4CPA, and A351 in 1BKX.
  
  
• Subset 3 is dipeptides which are deemed ligands by the policy of the World Wide Protein Data Bank. For more information, see above.
  
  See also anomalous atoms.

• The 20 historically standard L-amino acids, plus ambiguous residue codes ASX, GLX, and undetermined UNK.
• Actually, there are now 22 amino acids deemed "standard" for 3D structure models. In 2014, the Protein Data Bank included two additional genetically encoded proteogenic L-amino acids as "standard", namely pyrrolysine (PYL, O) and selenocysteine (SEC, U). In other contexts, those two additional amino acids may still be termed "non-standard".
• Twelve standard nucleotides A, C, G, I, T, U, DA, DC, DG, DI, DT, and DU plus UNK.
  The distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU) was first made when the PDB was remediated on August 1, 2007.

• D-amino acids are labeled "D", instead of the "X" used for other non-standard residues. To hide the D labels, see Labels.
• 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-" supercedes "D"). Example: 5e5t. (Click on "incomplete sidechains" in the Molecule Information Tab to put halos on S- residues.)
• Hydrophobic/Polar (Views tab) colors D-amino acids correctly.
• 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 and cation-pi interactions involving charged sidechains of D-amino acids. Examples are given in the lower left (help) panel.
• Protein crosslinks are detected for both D and L amino acids.

• This method works correctly only when all atoms (notably including the standard main-chain atoms) in non-standard residues are deemed HETATM in the PDB file. Examples include the many non-standard nucleotides in the t-RNA 1EVV (2MG, H2U, M2G, OMC, OMG, YG, PSU, 5MC, 5MU, 7MG, and 1MA), the non-standard seleno-methionines in 1H3O, and the non-standard phosphorylated serines and threonines in 1BKX. Typically, in these cases, the entire non-standard HETATM residue is given a non-standard PDB residue code name, such as MSE for selenomethionine, SEP for phosphoserine, or TPO for phosphothreonine. The corresponding full names can be seen in the MODRES or HETNAM records in the PDB file header (available from pdb.org, e.g. Header of 1EVV), or by clicking the PDB or OCA links in control panel (upper left) of FirstGlance.
  
  
• This method fails when an alternative convention is used in the PDB file: designating the standard main-chain atoms within a non-standard residue as ATOM, and only the non-standard atoms as HETATM. An example is GLY5 with PYL1005 in 1B07. In such cases, FirstGlance displays the non-standard portions of these residues as "Ligands+". (Many earlier such cases were fixed in remediations. For example, SER or THR plus PHO became SEP or TPO in remediated 1apm.)
  
  

1. rna (all RNA)
2. g, c (guanidylate and cytidylate in either DNA or RNA)
3. da, dt (adenylate and thymidylate in DNA; see standard residues)
4. (g,c) and rna (guanylate and cytidylate in RNA)
5. (a, t) and *.c5' (one atom per nucleotide). C5' is present in both ribose and deoxyribose.
6. (a, t) and phosphorus (nucleic acid backbone phosphorus atoms). Note that the 3' (hydroxy) terminal nucleotides have no phosphorus.
7. gly.ca (carbon-alpha in glycine)
8. met.sd (sulfur-delta in methionine)
9. mse (the group name for selenomethionine, e.g. in 1K28)
10. sulfur (all sulfur atoms; use full names for elements)
11. 12-23 (all residues/groups with sequence numbers in this range)
12. 12-23:b (residues/groups in chain B with sequence numbers in this range)
13. 12-23 and protein (excludes non-protein, such as water or DNA)
14. 12-23 and nucleic (excludes non-nucleic, such as water or protein)

• ~cyclic_nucleotides (or ~cyclic_nucs)
• ~unchained_nucleosides ("unchained" meaning not part of a polynucleotide)
• ~unchained_nucleotides ("unchained" meaning not part of a polynucleotide)
• ~unchained_aas ("unchained" meaning not part of a polypeptide)

1. If your PDB file contains multiple protein chains, decide which chain you are going to analyze for pI and charge.
2. Decide whether you want
   1. The values for the protein used in the experiment (crystallized or for solution NMR), which is often a fragment of the full-length protein, or
   2. The values for the full-length protein chain.
   
   To find out how much of the full length chain was deleted for the experiment, follow these instructions.
   
3. Obtain the one-letter sequence of the protein chain by clicking the Sequences link in the molecule tab (the tab labeled with the PDB code).
   1. Experimental fragment: use the OCA link.
   2. Full-length protein chain: use the UniProt link.
4. Copy the sequence and paste it into the large box at the Protein Calculator.
5. Check the three boxes under Charge at the right, and click Submit.

1. What are "atoms with halos"? Use the Find.. link (in any tab except Preferences) to apply halos to atoms that you specify. Halos are bright yellow (see snapshots at right -- touch snapshots with your mouse for more information).
   
   
2. Why aren't all residues in the chain selected? Non-standard residues (if any are present) are not selected when you click on a chain -- only the standard residues are selected. (Non-standard residues are colored slightly darker than the standard residues, but the same hue as the rest of the chain. You can highlight non-standard residues with a checkbox under Ligands+ or under Advanced/Technical in the Tools tab.) This has the advantage that you see the contacts between the standard residues (target) and the non-standard residues. If you wish to add the non-standard residues to the target, there are two methods.
   
   
   1. If there are only a few, change the selection mode to Residues/Groups and click on each of them.
      
      
   2. If there are many of them, use Find.. to put halos around the desired target. For example, you could enter a particular chain (prefix the chain name with a colon, such as :A for chain A), or protein, dna, or rna. (Even the non-standard residues will have halos.) Then enter Contacts.. and check Atoms with Halos. Next, Show Atoms Contacting Target. At this point, you can click Find.. and clear the halos, and then return to contacts (using the Return to Contacts link at the top of the lower left panel).
   
   
   Examples:
   • 1BKX has two non-standard residues in protein chain A.
   • 1EVV, a tRNA, has many non-standard residues.
   
   
3. Why can't I deselect by clicking on something already selected? In general, when you selected something by clicking on it, you can deselect it with a second click. For example, if the selection mode is "Chains" and you have already selected Chain A, clicking on Chain A again will deselect it. However, when you are clicking on something that is included in a larger selected set of atoms, it will not be deselected. For example:
   
   
   1. If Chain C is selected, and then you change the selection mode to "Residues/Groups", clicking on a residue in chain C will not deselect that one residue. Solution: To select large portions of a chain, use the "Range of residues in one chain" mode. Alternatively, Find the desired portion(s), for example "chain=B and (1-36 or 58-113)", and then, in the Contacts target selection dialog, check "Atoms with halos".
      
      
   2. If you have selected "Atoms with Halos", and the selection mode is "Residues/Groups", you cannot deselect atoms with halos by clicking on those atoms. Solution: Uncheck "Atoms with Halos". Now, with the selection mode set to "Residues/Groups", use the halos as a guide to click on the subset of groups with halos that you want.
   
   
4. How do I use sequence numbers to target a range of residues? Suppose you want to target the range of sequence numbers 22-33. In the Find.. dialog, enter "22-33" to put halos around the 12 residues from 22 through 33. Now click Contacts... There, check Target Atoms with Halos. Now you are ready to Show Atoms Contacting Target. If there is more than one chain with residues 22-33, for chain B, enter "22-33 and chain=B" in Find...

• Putative hydrogen bonds: nitrogen or oxygen atoms that are within 3.5 Å of nitrogen or oxygen atoms within the target. Protein hydrogen bonds with donor-acceptor distances of less than 3.2 Å are energetically significant. When donor-acceptor distances exceed 3.5 Å, the bond energy falls to questionable significance. More about hydrogen bonds. A hydrogen bond between a donor-acceptor pair within 3.5 Å requires the presence of a hydrogen atom between the donor and acceptor, and suitable angles between the donor proton and the lone electron pair on the acceptor. Examination of hydrogen atom positions is quite helpful. Nevertheless, what appear to be energetically significant hydrogen bonds may not meet stringent angular criteria (Morozov et al., 2004; see example below).
  
  
  • Simple example of hydrogen bonds: Either protein chain in 1D66 recognizes the DNA sequence CGG through hydrogen bonds.
    
    
  • Hydrogens can be added to PDB files lacking them by the MolProbity server (see link under Key Resources). After saving the resulting model to disk, it can be uploaded for examination in firstglance.jmol.org. Be cautious, however, because the accuracy of donor-acceptor distances and angles depends on the resolution and local disorder. Be sure to examine your structure with Local Uncertainty under the Views tab.
    
    
  • Example of non-bonds: What appear to be hydrogen bonds in the "dry interface" in the amyloid-like fiber structure reported by Nelson et al. (2005) (see Figures rendered in Jmol) were determined not to be such after careful examination of the angles (David Eisenberg, personal communication).
• Water and water bridges.
  
  

  Water bridge in 1D66 between the sidechain nitrogen of Arg 46 (chain B) and a phosphate oxygen of Arg 46 in Cytosine 13 (chain D).

  In the Contacts Shown display, hydrogen bonds in which one partner is water can be displayed separately from hydrogen bonds in which neither partner is water.
  
  Furthermore, water bridges can be shown separately (a subset of hydrogen bonds involving water). Each bridge includes at least these three atoms:
  1. A target oxygen or nitrogen within 3.5 Å of a non-target water oxygen.
  2. The bridging non-target water oxygen.
  3. A non-target, non-water oxygen or nitrogen within 3.5 Å of the bridging water.
  
  Examples:
  • In 1D66 (Gal4 bound to DNA), protein chain A has a single water bridge, going to DNA. DNA chain D has four water bridges to DNA chain E.
  • In 1BL8, the potassium channel, target any chain in Contacts.. and display only the water bridges. There is a single water in the channel which bridges the four chains. (There are also nice cation-pi interactions between chains.)
  • In 1LCD, numerous waters with hydrogens bridge the protein to the DNA.
• Van der Waals interactions. Carbons, sulfurs, or seleniums within 4.0 Å (see Note* below) of carbons, sulfurs, or seleniums within the target. These are sufficiently close for energetically significant van der Waals "hydrophobic" interactions, and include C-C (including aromatic ring-stacking), C-S, C-Se, and S-S interactions (including disulfide bonds between target and contacting atoms, for example, between the two heavy chains in antibody 1IGT).
  
  Simple examples of hydrophobic interactions:
  • The two chains of 1D66 contact each other forming a small, buried, hydrophobic core.
  • The ring stacking contacts to any deoxynucleotide base in the DNA in 1D66.
  • The contacts to heme (HEM) in 2HHD.
    
    
  • *Note: The distance cutoff was 4.5 Å until version 1.46 of FirstGlance in Jmol (released June 17, 2012). Several crystallographers recommended that this distance be reduced to 4.0 Å.
  
  
  
• Salt bridges: Sidechain nitrogens (arg.ne,arg.nh?,lys.nz), or N-terminal nitrogens, with a full electronic positive charge at neutral pH within 4.0 Å of sidechain oxygens (asp.od?,glu.oe?) or C-terminal oxygens with a full electronic negative charge at neutral pH. More about salt bridges.
  
  There are two ways to visualize protein salt bridges in FirstGlance: (i) Contacts.. shows them between a target you select and the remainder of the model; (ii) Salt Bridges/Cation-Pi.. (in the Tools tab) enables you to find them throughout the model. Salt bridges where one or both partners is not a standard amino acid are not shown in these views.
  
  
  • Example: Each chain in 2hhd has one salt bridge in each direction between chains A and C. Further examples are described in the lower left (help) panel when you use Salt Bridges/Cation-Pi (Tools tab).
    
    
  • Oxygens missing at carboxy termini: It is fairly common that authors of crystallographic models (PDB files) leave out one of the oxygens on the carboxy termini of protein chains. Such carboxy termini, missing one oxygen, are marked ¶ by FirstGlance in its Ends report (Molecular Information tab or Tools tab). Examples: 1bl8, 2xy9, 1bl8, This is legal according to the PDB format requirements (information from Rachel Kramer Green of RCSB, November, 2017), and the missing oxygen is not listed in REMARK 470 which lists other missing atoms.
    
    When one of the carboxy-terminal oxygens is missing, FirstGlance detects salt bridges by looking for a cationic sidechain within 5.2 Å of the carboxy carbon atom. An example is 5j0z, where the carboxy-terminal Phe315 is salt-bridged to Arg118. When this molecule is processed in FirstGlance's Salt Bridges/Cation-Pi (Tools tab), the terminal carboxy carbon is represented as a ball to indicate its participation in a salt bridge. In Salt Bridges lower left (help) panel, click "Show halos on: All Protein Chain Termini" to highlight the ends of chains, making it easy to find carboxy-termini engaged in salt bridges. Other examples: 6nie. (Technical: Measurements leading to the choice of 5.2 Å will be found in saltbr.txt. Code is in makeSB_CTermNoOXTCarbonsSpt() in scripts.js.)
• Cation-pi interactions: Cationic sidechain nitrogens (lysine or arginine), or cationic protein chain amino-termini, within 6.0 Å of the face of an aromatic ring (phenylalanine, tyrosine, or tryptophan) may engage in polar interactions called "cation pi interactions" (Gallivan & Dougherty, 1999). These play an important role in the overall energetics of protein folding. For a brief introduction, see More about cation-pi interactions.
  
  There are two ways to visualize cation-pi interactions in FirstGlance: (i) Contacts.. shows them between a target you select and the remainder of the model; (ii) Salt Bridges/Cation-Pi.. enables you to find them throughout the model. Cation-pi interactions where one or both partners is not a standard amino acid are not shown in these views.
  
  
  • FirstGlance displays putative cation-pi interactions based on the cation being within 6.0 Å of three alternate carbons in an aromatic ring. FirstGlance will fail to show some energetically significant cation-pi interactions, and some that it shows will not be energetically significant. Please see the CaPTURE server for an authoritative listing of sidechain cation-pi interactions.
    
    CaPTURE does not report cation-pi interactions involving cationic amino termini of protein chains, but FirstGlance does display them.
    
    When the model is large, in order to save time, FirstGlance uses a faster but somewhat less accurate method of detection than is used for the smaller 90% of entries in the PDB. (The faster method is used for models with >12,000 non-hydrogen atoms, which are the largest ~10% of entries in the PDB.) The faster method sometimes shows lysine or arginine without a contacting aromatic ring, or vice versa, and sometimes shows pairs that fail the strict 6.0 Å criterion (see more details in catpi.txt).
    
    This is because the faster method looks for three aromatic ring atoms within 6.0 Å of the cation, but cannot tell if the three are in the same ring. An example is 2hhd, where ARG141 in chains A and C are displayed without ring partners. This is because both TYR35 and TRP37 have ring atoms within 6.0 Å, but neither ring has three such atoms. (CaPTURE deems the interaction with TRP37 to be energetically significant, despite its failing the 6.0 Å rule.)
    
    The slower, more accurate method applies the 6.0 Å test residue-by-residue.
    
    A more complicated example is 2v61. This example has only ~9,000 atoms, so it defaults to the slower, more accurate method, but the results of the faster method have been compared. The faster, less accurate method displays 4 aromatic rings without nearby cations, and three cation-pi residue pairs that fail the stricter, slower method. The faster, less accurate method reports 20 cations and 22 rings, while the slower, more accurate method reports 17 cations and 16 rings. See catpi.docx for details.
    
    
  • Neither FirstGlance nor CaPTURE will report cation-pi interactions where the cation or aromatic ring are not standard amino acid components. Examples include metal cations, or aromatic rings in ligands. FirstGlance can, however, show the contacts for any moiety, so you could select metals or ligand aromatic rings, and visualize their contacts.
    
    
  • Examples are provided at the bottom of the lower left help panel when displaying cation-pi interactions. Here are a few more:
    • One end of peptide chain P in 2VAB contains PHE1:P interacting, in an energetically significant manner according to CaPTURE, with LYS66:A.
    • Each chain in the homotetramer 1BL8 has one cation-pi interaction with each of the two chains it contacts. These are deemed energetically significant by CaPTURE.
    • The peptide chain C has one energetically significant cation-pi interaction with chain A in 1B07.
    • Firstglance finds two LYS:PHE cation-pi interactions, one in each direction, between chains B and D in 1IGT. CaPTURE is unable to handle PDB files that contain "inserted" sequence numbers, and this includes 1IGT. However, if the PDB file is renumbered (with RasMol) and saved, then uploaded to CaPTURE, results are obtained. CaPTURE deems neither of the proximities detected by FirstGlance as energetically significant.
• Metal and miscellaneous bonds include three categories of distance-based atom pairs.
  1. Sulfur atoms within 3.2 Å of a metal atom (presumed to be a cation). "Metal" is defined as any metal that occured in the Protein Data Bank in April, 2013 (orignal list was from April, 2006), which include the following:
     The following elements did not occur in the Protein Data Bank in April, 2013. Sulfurs interacting with these would not be displayed.
     • francium
     • Alkaline earths: radium
     • Transition metals: niobium
     • Lanthanides: neodymium, promethium, dysprosium, thulium
     • Actinides: actinium, thorium, protactinium, neptunium, plutonium, americium
     Elements not listed above were not considered.
     
     
  2. Any atom outside the target that is not (carbon, sulfur, phosphorus, or hydrogen) within 3.5 Å of any atom within the target that is not (carbon, sulfur, or hydrogen); and vice versa. Atoms deemed to be involved in putative hydrogen bonds (see above) are then excluded. The resulting set includes, for example, O-metal, Se-metal, and metal-to-metal interactions, as well as chloride ion interactions with polar moieties, but excludes metal ions interacting with sulfurs.
     
     
  3. Any atom outside the target that is not (carbon, sulfur, phosphorus, or hydrogen) within 3.5 Å of any metal atom within the target; and vice versa. This finds atoms such as nitrogen or oxygen that are probably bound to metals, regardless of whether they may also appear to be involved in hydrogen bonds. The resulting set includes, for example, the sidechain nitrogen in HIS bound to Fe⁺⁺ in heme.
     
     
  4. Any atom outside the target that is not (carbon, oxygen, nitrogen, sulfur, phosphorus, or hydrogen) within 4.5 Å of any atom in the target, or vice versa. This includes, for example, metal or chloride ions interacting with any element, and Se-C or Se-S interactions. This rule is also intended to display interacting elements not anticipated by the preceding rules.
  
  
  Examples (using Contacts..):
  • Targeting either a protein chain in hemoglobin 2HHD, or a heme group, or an iron atom in a heme, shows the histidine sidechain nitrogen interacting with the Fe⁺⁺.
  • Targeting either one cadmium atom or one protein chain in 1D66 reveals the cadmium-sulfur bonds, and the cadmium-cadmium proximity.
  • Targeting the three potassium ions in 1BL8 reveals their bonds to nearby oxygens.
  • Targeting the three potassium ions in 1KF1 reveals their anhydrous bonds to DNA oxygens.
  • 1IXJ includes DNA, water, CoN₆H₁₈ (cobalt hexamine) and MgO₆H₁₂ (magnesium hexahydrate).
    
    

• Hydrogen in Contacts Shown: In the "Contacts Shown" display, only those hydrogens bonded to contacting atoms (balls) are shown. (Hydrogens bonded to non-contacting atoms [sticks] are not shown.) Hydrogens are shown as sticks connected to balls to make the angles of these bonds clear.
  
  
  • Example: Select the single sodium ion in 1LCD as target, and show its contacts. Hydrogens are hidden by default to simplify the Contacts Shown display. Check the checkbox "Show hydrogens" in the lower left (help) panel. The hydrogens on the waters contacting the Na⁺ ion point away from it, consistent with the metal ion binding to lone electron pairs of the water oxygens.

• Only models with resolutions of 4.0 Å or better are analyzed. If the PDB file has no header section and therefore the resolution is not known, it is analyzed.
• Only conformation 1 is analyzed and displayed (when alternate locations are present).
• Only model 1 is analyzed and displayed (when multiple models are present).
• Criteria are intentionally broad, and will detect some proximities that are not actually the type of bond suggested as putative or possible, often clashes. Thus, detailed examination including the electron density map is crucial. Nevertheless, legitimate bonds will sometimes fail to be detected because they have unrealistically long bonds that fall outside the maxima used by FirstGlance (see examples below).
• Technical: makeFindCrosslinksSpt() in scripts.js. showCrosslinksHelp() in help1.js. showCrosslink() in scripts.js. crosslinkType.
  
  
• CAUTION: Models predicted by AlphaFold may have clashes that are suggested as putative crosslink bonds. Models determined by electron microscopy may have many clashes, or covalent bond lengths too long to be detected with the cutoff distances used by FirstGlance. For example, 6nef and 6ef8 are independent electron microscopic determinations of the same protein (outer membrane cytochrome S of Geobacter sulfurreducens). Each heme (HEC) is bonded to 2 cysteines via thioether links. In 6ef8 (nominal resolution 3.7 Å), all such thioether links are detected, with bond links ranging from 1.75 to 2.13 Å. However in 6nef (nominal resolution 3.4 Å), half of the thioethers are detected with bond lengths 1.78-1.86 Å, while the other half are not because they have chemically unrealistic bond lengths 2.54-2.87 Å.
  
  
• Isopeptide crosslinks. Methods:
  1. Lysine sidechain nitrogen (Lys/Dly NZ) within 2.1 Å of a carbon atom that is covalently bonded to a non-water oxygen atom.
  2. Arginine* sidechain nitrogen (Arg/Dar NH?/NE) within 2.1 Å of a carbon atom that is covalently bonded to a non-water oxygen atom.
  3. Any carbon, not in Lys, Arg, Dly, or Dar, that is within 2.1 Å of a nitrogen atom identified in steps 1 or 2 above
  4. For partner carbons identified in step 3 above:
     1. If the partner group is Glu/Gln/Dgl/Dgn, sometimes both CG and CD are within the cutoff distance. Then, CG is ignored. Example: 5VBL.
     2. If the partner group is Asn/Asp/Dsg/Das, perhaps both CB and CG could be within the cutoff distance. Then, CB is ignored. Example: none known.
     3. If the partner group is none of the Gl?/As? family, it is likely a C-terminal residue. Sometimes both C (main chain terminus) and CA are within the cutoff distance. Then, CA is ignored. Example: 7CAP.
  5. Asparagine/Aspartate (Asn/Asp/Das/Dsg) distal sidechain carbon (CG) within 2.1 Å of a nitrogen atom (not in Asn/Asp/Das/Dsg).
  6. Glutamine/Glutamate (Gln/Glu/Dgl/Dgn) distal sidechain carbon (CD) within 2.1 Å of a nitrogen atom (not in Gln/Glu/Dgl/Dgn).
  7. Any nitrogen, not in Asn/Asp/Das/Dsg/Gln/Glu/Dgl,Dgn, that is within 2.1 Å of a carbon identified in steps 5 or 6 above.
  ⊳ Example: 2xi9. Additional examples are listed in the Lower Left Panel for this example.
  ⊳ Basis for 2.1 Å cutoff: 17 PDB files containing isopeptide bonds have isopeptide bond lengths of 1.3-1.6 Å (resolution average 2.0, range 0.9 - 2.9 Å). A rare outlier, 2x9x (resolution 1.5 Å) has three isopeptide bonds, both according to the publication (Spraggon et al., 2010) and the PDB file (COMPND OTHER_DETAILS). The electron density map confirms these three bonds. However, their isopeptide bond distances are unrealistic at 2.0, 2.2, and 2.9 Å. The cutoff was set to detect some outliers without producing too many spurious "detections".
  ⊳ *No bona-fide examples involving Arginine are known to the However, FirstGlance will report clashes between Arg sidechain nitrogens and carbons in carbonyls as possible isopeptide bonds.
  ⊳ Technical: select ~isopeptide_bonds.
  
  
• Thioester crosslinks. Method:
  1. Cysteine sidechain sulfur (Cys/Dcy SG) within 2.3 Å of a carbon atom that is covalently bonded to a non-water oxygen, and is not in Cys or Dcy.
  Example: 2xi9. Additional examples are listed in the Lower Left Panel for this example.
  Technical: select ~thioester_bonds.
  
  
• Thioether crosslinks. Method:
  1. Cysteine sidechain sulfur (Cys/Dcy SG) within 2.3 Å of a carbon atom that is NOT covalently bonded to a non-water oxygen, and is not in Cys or Dcy.
  2. When Cys/Dcy is thioether bonded to carbons CAB/CAC in HEC (heme), sometimes carbon C3C falls within the cutoff distance of 2.3 Å, in which case it is ignored. Example: 6ef8.
  ⊳ Example: 6e87 (sulfur-carbon distance 1.83 Å).
  ⊳ Example with unrealistic bond lengths: 6nef is a cryo-EM model with 6 hemes. There are two thiether bonds to each heme. Half of those bonds (the ones to carbon CAB on each heme) have realistic lengths of 1.78-1.86 Å. The other half (to CAC on each heme) have unrealistically long bonds lengths of 2.54 to 2.87 Å, and those fail to be detected by FirstGlance.
  ⊳ Additional examples are listed in the Lower Left Panel for this example.
  ⊳ Technical: select ~thioether_bonds.
  ⊳ Basis for 2.3 å cutoff: Although most thioether models have S-C distances of 1.7-1.9 Å, the thioethers Cys93-Tyr157 in 6u4s or 4kwj have sulfur-carbon distances of 2.05 Å. (In 6u4s, PDB-REDO increases it to 2.72 Å.) Therefore, the detection cutoff was relaxed to 2.3 Å. However, some still fail to be detected due to unrealistically long bond lengths (see 6nef above).
  
  
• Ester crosslinks. Method:
  1. Threonine sidechain oxygen (Thr/Dth OG) within 2.1 Å of a carbon atom (not in Thr/Dth).
  2. Serine sidechain oxygen (Ser/Dsn OG) within 2.1 Å of a carbon atom (not in Ser/Dsn).
  3. If the partner group is a C-terminal residue, sometimes both C (main chain terminus) and CA are within the cutoff distance. Then, CA is ignored. Example: 2PNL.
  Example: 4mkm. Additional examples are listed in the Lower Left Panel for this example.
  The welcomes more examples with ester crosslinks.
  Technical: select ~ester_bonds.
  
  
• Histidine-tyrosine crosslinks. Method:
  1. Histidine sidechain nitrogen (His or Dhi) within 2.2 Å of a tyrosine (Tyr or Dty) sidechain carbon atom.
  ⊳ Example: 1v54. Additional examples are listed in the Lower Left Panel for this example.
  ⊳ welcomes more examples with His-Tyr crosslinks.
  ⊳ Technical: select ~histyr_bonds.
  ⊳ Basis for cutoff: Although most models with His-Tyr bonds have N-C distances of 1.3-1.7 Å, the distance is 2.05-2.06 Å in 1gge. Therefore, the detection cutoff was relaxed to 2.2 Å.

• Lysine-cysteine NOS crosslinks. Method:
  1. Cysteine sidechain sulfur (Cys/Dcy SG) or sidechain sulfur of S-hydroxycysteine (CSO.SG) within 3.1 Å of a nitrogen atom, which is not a main chain nitrogen, and is in none of Asn/Gln (or their D forms Dsg/Dgn).
  2. The maximum cutoff of 3.1 Å is slightly more generous than the maximum of 3.0 Å used by von Pappenheim et al.. Also, they limited their scan of the PDB to models with resolutions of 2.0 Å or less, while FirstGlance reports S-N proximities in models with resolutions of 4.0 Å or less.
  Example: 6zx4. Additional examples are listed in the Lower Left Panel for this example.
  Technical: select ~NOS_bonds.

• An ALERT is a message that appears in a pop-up box and must be acknowledged before anything else can be done.
• appears below the molecule when any of the Unusual components or features listed below are present.
• Under Find:, terms beginning "~" (tilde) are defined by FirstGlance. They are not built into Jmol.

Clicking on the halos ALL UNUSUAL components or features

1. Single/monomeric amino acids, not part of a polymer. Classified as ligands. Listed under Ligands+ and Non-Standard Residues in the Molecule Information Tab. Examples: 4ffL, 4reo. Find: ~unchained_aas
2. Dipeptides, which are classified as ligands. Listed under Ligands+ and Non-Standard Residues in the Molecule Information Tab. Examples: 4d2c, 1dpp. Find: ~dipeptides
3. D amino acids. Examples: 2soc, 1al4. To hide the D labels, see Labels. Find: ~d_aas
4. Ribothymidine (5-methyl uridine). Examples: 5MU in 1evv and 1i9v. Find: T and RNA
5. Deoxyribouridine. Example: DU in 1g22. Find: U and DNA
   
   Protein Crosslinks:
   The existence of any of the following unusual protein crosslinks triggers an alert, regardless of the preference setting.
6. Isopeptide crosslinks. Example: 3htl. Find: ~isopeptide_bonds
7. Thioester crosslinks. Example: 2xi9. Find: ~thioester_bonds
8. Thioether crosslinks. Example: 6e87. Find: ~thioether_bonds
9. Ester crosslinks. Example: 4mkm. Find: ~ester_bonds
10. Histidine-tyrosine crosslinks. Example: 1v54. Find: ~histyr_bonds
11. Lysine-cysteine NOS bonds. Example: 6ZX4. Find: ~NOS_bonds
    
    
12. GLX or ASX (ambiguous) residues. Example: 1kp0. Find: GLX or ASX
13. Unknown atoms X. Example: 1kp0. Find: *.x??
14. Unknown atoms or groups UNX or UNK. Examples: 5wbn, 5g4a, both in 3hm6. Find: UNX or UNK
15. Unknown nucleotides "N". Examples: in polymer chain, 2i82; not in polymer, 3dzi. Find: [n]
16. Unknown ligands "UNL". Examples: 6eqq, Find: UNL
17. Anomalous atoms. Example: none known. Find: ~anomalous_atoms
    
    
18. Amino acids lacking alpha carbon atoms. Example: Thr918 in 1h3o, and Lys214 in 2fd8 have only a nitrogen atom. Find: ~nobackbone_aas
19. Amino acids lacking peptide-bonding atoms. Example: Gln8 in 4en3. is missing a main chain nitrogen atom. Find: ~unbondable_aas
20. Amino acids lacking main chain oxygens. Examples: Gly5 in 1b07; Met79 in chain M in 1uc5. Find: ~nomainchaino_aas
    
    
21. Single nucleoSide (no phosphate), not part of a polymer of standard nucleotides. Example: A351 in 1bkx. Find: ~unchained_nucleosides
22. Single nucleoTide (has phosphate), not part of a polymer of standard nucleotides. Examples:
    • Adenosine monophosphate (AMP) phosphodiester-bonded to 7BV in 5gyz.
    • Adenosine monophosphate (AMP) bound to Zinc in 5gz5.
    • Adenosine 5' monophosphate (AMP) non-covalently bound to protein in 5udt.
    • Adenosine 2' monophosphate (the common form is 5' phosphorylated) in 5udt.
    • Adenosine diphosphate (ADP) bound to Mg in 6b8b.
    • Adenosine diphosphate (ADP) non-covalently bound to protein in 6bLb.
    • Adenosine 5'-triphosphate (ATP) in 5g4a.
    • Guanosine di- and tri-phosphate (GDP, GTP) non-covalently bound to protein and Mg in 5nd4.
    Find (includes cyclic nucleotides): ~unchained_nucleotides
    
    
23. Cyclic nucleotides. Examples:
    • Cyclic-AMP (CMP) non-covalently bound to protein in 5kjx.
    • Cyclic-GMP (PCG) non-covalently bound to protein in 5c8w.
    • 2',3'-cyclic AMP (ACK) in 2ype.
    • Additional examples of cyclic nucleotides.
    Find: ~cyclic_nucs
    
    
24. Insertion codes (see Unusual sequence numbering). Example: 1igy. Find (^ means the following character is an insertion code; "?" means any insertion code): ^?
25. Zero or negative sequence numbers. Examples: 1d5t, and see others in Unusual sequence numbering. Find: resno < 1

26. When any of the above-listed unusual protein crosslinks are present. Example: 2xi9.
27. When protein is modeled with only alpha carbon atoms, or nucleic acid chains are modeled with only backbone phosphorus atoms. Examples: protein in 1a1d, protein and DNA in 1bdx. Find: click on below the molecule.
28. When missing residues are not marked with empty baskets because nearby residues with coordinates (upon which to "hang" the empty baskts) were not found. Example: 4o46.
29. When the number of models given in the NUMMDL record does not agree with the number of conformers submitted in REMARK 210. Example: none known. (Examples found earlier have been corrected by the PDB.)
30. When there are >100 incomplete sidechains. See label S- for examples.

• Missing residues. Count reported in the Introduction and in the Molecule Information Tab, where a link reports the missing sequence numbers in each chain. Example: 1d66. Find: cannot be found since they are absent in the model. Indicated in FirstGlance by "empty baskets".
• Incomplete (Missing) sidechains. Count reported in the Introduction and in the Molecule Information Tab. Labeled with S- in the molecular display. Examples: see incomplete sidechains. See also label S- for examples with >100 incomplete sidechains, cases that are alerted because the S- labels will be hidden to reduce clutter. Example: 2ace. Find alpha carbons: ~incomplete_sidechains. Find all atoms in residues with incomplete sidechains: ~incomplete_sidechain_residues.
• Missing beta carbons are reported in the Molecule Information Tab, in "more details" mode only. Example: 1ijw.
• Unusual chemical elements are reported in boldface in the Molecule Information Tab under the atom count, with a link that reports counts of atoms of each chemical element present. Example: 1ihu. Find: click on the element count in the Molecule Information Tab to display Chemical Elements with counts. Click on an element to find it.
• The count of atoms with alternate locations is given in the Molecule Information Tab under the atom count, in "more details" mode only, with a link that provides an explanation, and a link to Find alternate locations. Example: 1bsz.
• Non-standard amino acids or nucleotides are listed in the Molecule Information Tab along with the count of each. Examples: protein, 3c1p; RNA, 1evv. Find: Each is clickable in the listing, or to find all: ~nonstandard_residues

Rationale: According to the rules for PDB files, all atoms that are not members of standard residues in protein or nucleic acid chains should be designated "hetero". Hetero atoms are typically further subdivided: there is "solvent" (water and some inorganic anions such as sulfate and phosphate), and everything else is "ligand". Rare PDB files don't follow the rules, and these confuse Jmol. The result is atoms that are neither protein, nucleic acid, nor hetero. Within FirstGlance, these are deemed anomalous atoms.

Missing main chain atoms. Such cases could result from lack of electron density, or simply from errors in published PDB files.
• THR918 in 1H3O, and ALA333:C in 1PRC lack all atoms except the peptide-bonded nitrogen.
  
• The main chain oxygen (.O) is missing from GLY5 in 1B07, and MET79:M in 1UC5.
  
  
• 1GRH, in its original form, had only two residues, CYS and EOH (ethanol), with the ethanol covalently linked to the CYS sulfur. Formerly, CYS atoms were ATOM, and EOH was called HEC with HETATM. After one stage of remediation, the CYS was deemed HETATM. In the current (early 2013) remediation, the entire protein has been added, leaving CYS 48 as ATOM and EOH as HETATM (see the end of REMARK 3). FirstGlance shows the EOH as Ligand+.
  
  
• Entries containing D amino acids: (See above for how these are now handled correctly.)
  • 2SOC. is an octapeptide of (from SEQRES) DPN CYS PHE DTR LYS THR CYS THO.
  • 1AL4: FOR0, VAL1, ILE1, GLY2, continuing (without further sequence number anomalies) ALA3 DLE ALA DVA VAL DVA TRP DLE TRP DLE TRP DLE TRP ETA17. Note that both VAL1 and ILE1 occupy the same physical position in the chain sequence. This represents sequence microheterogeneity in the protein that was crystallized. By convention, the ILE1 is not listed in SEQRES. Neither has an insertion code (column 27), but instead they are indicated to be alternate conformations (A and B in column 17; see PDB Format 3.2). FirstGlance handles this entry correctly.

• When tested in 2019 & 2021, spinning and rotation-by-mouse of spacefilled (solid) representations, when zoomed large, was slower and jerkier then other browsers. Therefore, although rotation of cartoon representations is OK, the other popular browsers will perform better overall.

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