• X marks non-standard residues.
• S- marks incomplete Sidechains.
• ? marks anomalous atoms.

• 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 (PHO) of serine and threonine 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. [More..]
  
  Examples include GLY308 in 4CPA, and A351 in 1BKX.
  
  See also anomalous atoms.

• The 20 standard amino acids, plus ambiguous residue codes ASX, GLX, and undetermined UNK.
• 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.

• 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)

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.
      
      
   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, append a colon followed by the chain name you want. For chain B, enter "22-33: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 the phosphate 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 with a full electronic positive charge at neutral pH (arg.ne,arg.nh?,lys.nz) within 4.0 Å of sidechain oxygens with a full electronic negative charge at neutral pH (asp.od?,glu.oe?). 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.
• Cation-pi interactions: Cationic sidechain nitrogens (lysine or arginine) 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). 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 possible 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 a reliable listing of cation-pi interactions in any PDB file.
    
    Occasionally, FirstGlance will show lysine or arginine without a contacting ring (a bug). FirstGlance's present routines look for three ring atoms within 6.0 Å, 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.
    
    
  • 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:
    • 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. 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.

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. And rarely, Jmol may interpret PDB files incorrectly. 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:
  • 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.

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  (Chrome out-performed Firefox in 2014, but changes in Chrome in 2015 impaired its operation of JSmol.)

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• Firefox runs JSmol (no Java) substantially faster than any other browser in both Windows and OS X. Therefore Firefox is recommended for JSmol.
  
  
• Firefox works well with Java.

• JSmol (no Java):
  • Windows: Maxthon is satisfactory. Spinning and rotation by mouse were almost as good as in Firefox.
  • Mac OS X: rotation by mouse in Maxthon was jerkier than in Firefox. Therefore, Firefox is recommended for JSmol in OS X.
  
  
• Java: Maxthon supports Java well in Windows. There is no Java support in the OS X version (May, 2016).

• JSmol: Spinning is as smooth as in Firefox, but rotation by mouse is jerkier. Therefore, Firefox is recommended for JSmol in OS X.
  
  
• Java: Safari supports Java.

• JSmol (no Java): In 2015-2016, Opera ran JSmol satisfactorily in Windows. In OS X, rotation of the molecule is unacceptably slow and jerky. Therefore, Firefox is recommended for JSmol in OS X.


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