Notes for FGiJ

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Notes for FirstGlance in Jmol

Contents

How to Use FirstGlance

Identifying atoms
Measuring distances and angles
Sequences of protein or nucleic acid chains
Advanced uses of Find..
FAQ for Contacts..

Understanding FirstGlance: Definitions
The twenty standard amino acids
Hydrogen in macromolecular models
Definition of Ligands+
Definitions of protein, DNA, RNA, carbohydrate
Definitions of non-standard residues
Definitions of "contacting" atoms and properties of non-covalent bonds
Labels on contacting atoms
Anomalous atoms

Browser Peculiarities
Firefox
Safari

Technical
Java
Uploading PDB files

For topics not covered here, see All About FirstGlance in Jmol.

Clicking on an atom produces an identification report in the Jmol rectangle, to the lower left of the molecule (see snapshot at right), and also in the browser's status bar. (In Firefox on Mac OSX only, you often have to click twice before the report is produced.) Amino acids are reported as 3-letter abbreviations, and nucleotides as A, C, G, T, or U. Ligands and non-standard residues have other abbreviations. If you don't recognize the abbreviation, click on the PDB icon (upper left panel in FirstGlance), and there, the Biology & Chemistry tab, and look under Ligands and Prosthetic Groups; or click the OCA icon (upper left panel in FirstGlance), and look under ligand.

Atoms are identified using PDB file format nomenclature, as follows:

Amino Acids C, N, O = main chain
CA = Carbon, Alpha
CB = Carbon, Beta
CG, OG = Carbon/Oxygen, Gamma
CD = Carbon, Delta
NE, OE = Nitrogen/Oxygen, Epsilon
NZ = Nitrogen, Zeta
NH = Nitrogen, Eta

Nucleotides P, O1P, O2P = phosphate
O3*, O5* = 3' and 5' pentose oxygens
C1* to C5* = 1' to 5' pentose carbons
C2-C8, N1-N9, O2-O6 = elements in bases
C5M = C5 Methyl (in Thymine)

In addition to clicking, you can simply touch an atom with the mouse (without moving the mouse, which is called "hovering"), and after a delay of about two seconds, a yellow message will appear near the mouse pointer (see snapshot at right) with an atom identification report. This works best with Spin off.

not

Java

FirstGlance in Jmol depends entirely upon the Jmol java applet to render its molecular views. In order for Jmol to work properly, it requires a support program called a java virtual machine. Computer operating systems (such as Windows, Mac OSX, and linux) generally come with java included, but it may be an out of date version. It is generally advisable to keep your java up to date, which can be done by visiting java.com. Some Windows computers have no java at all, until you visit java.com.

Whether your browser has java, and if so, what version, is reported by visiting javatester.org.

Amino Acids

Here are the twenty standard amino acids, with their three and one-letter abbreviations. Mnemonic names may help you to remember the one-letter codes, but are not the correct names.

Ala A Alanine Arg R Arginine Asn N Asparagine Asp D Aspartic acid (mnemonic: asparDic) Cys C Cysteine Gln Q Glutamine (mnemonic: Quetamine) Glu E Glutamic acid (mnemonic: gluEtamic) Gly G Glycine His H Histidine Ile I Isoleucine Leu L Leucine Lys K Lysine (mnemonic: liKesine) Met M Methionine Phe F Phenylalanine (mnemonic: Fenylalanine) Pro P Proline Ser S Serine Thr T Threonine Trp W Tryptophan (mnemonic: tWyptophan) Tyr Y Tyrosine Val V Valine

Sequences and Gaps

Sequences of amino acids or nucleotides can be viewed by any of these means:
- PDB button, then the Sequence Details tab near the top right. These are annotated, one-letter sequences with links to other resources.
- OCA button, then look below in the Sequence-derived information section for one-letter sequences in FASTA format plus links to other resources.
- available via the OCA button. At OCA, use the link SEQRES to COORDINATES.
Gaps: S2C (SEQRES to Coordinates) is particularly valuable for 3D structural data (but currently provides no information for nucleic acids). It lists the sequence of the protein used in the structure-determination experiment, aligned with the sequence of the amino acids given coordinates. Often, in crystallographic experiments, some amino acids are disordered in the crystal, and no atomic coordinates are provided for these. Such gaps in the structure data are shown as deletions in the coordinates column of the alignment, highlighted in red in these excerpts from the S2C output for 2ACE.
- Columns S represent the sequence of the protein used in the experiment (from SEQRES records in the PDB file header);
- Columns C are the sequence of amino acids with Coordinates (from ATOM records in the PDB file).
```
         ***** SAMPLE FOR 2ACE *****
            S   C     S      C
SEQCRD 0 D ASP ---     1      - - - 367       Key to 3-Letter Codes
SEQCRD 0 D ASP ---     2      - - - 367    
SEQCRD 0 H HIS ---     3      - - - 367       THIS LISTING IS NOT FOR YOUR MOLECULE!
SEQCRD 0 S SER SER     4      4 C T 5         EXAMPLE AT LEFT IS FOR 2ACE.
SEQCRD 0 E GLU GLU     5      5 C T 5         FOR YOUR MOLECULE, 
  [lines 6-482 omitted]                       SEQCRD 0 N ASN ASN   483    483 C T 5      
SEQCRD 0 E GLU GLU   484    484 C T 5      
SEQCRD 0 P PRO ---   485      - - - 367    
SEQCRD 0 H HIS ---   486      - - - 367    
SEQCRD 0 S SER ---   487      - - - 367    
SEQCRD 0 Q GLN ---   488      - - - 367    
SEQCRD 0 E GLU ---   489      - - - 367    
SEQCRD 0 S SER SER   490    490 C T 5      
SEQCRD 0 K LYS LYS   491    491 C T 5      
  [lines 492-533 omitted]
SEQCRD 0 A ALA ALA   534    534 H H -      
SEQCRD 0 T THR THR   535    535 H C 5      
SEQCRD 0 A ALA ---   536      - - - 367    
SEQCRD 0 C CYS ---   537      - - - 367    
```
The conclusion from the above listing is that residues 1-3, 485-489, and 536-537 lack coordinates. In a long S2C listing such as the one above, you can use your browser's Find in page with the search word "---" to jump to any gaps.

View 2ACE in FirstGlance, click N->C Rainbow, and then paste this line
```
4, 484, 490, 535
```
into the Find.. slot and press Enter. You will be able to see the gap in the chain, marked by halos. By clicking on the beginning and end of the chain (marked with halos) you will see that the chain does not start at 1, nor does it end at 537. Notice that without examining the S2C listing, it would have been easy to overlook the missing residues in the crystallographic model.

It is envisioned that a future version of FirstGlance may have a built-in sequence listing that incorporates the information from S2C. Clicking on a residue in the proposed listing would highlight that residue in the 3D molecular view. Specifications have been developed. Implementation is not trivial. Interested volunteer programmers are invited to contact the

Thanks to Guoli Wang and Roland L. Dunbrack for providing the S2C server, and to Jaime Prilusky for providing the above-linked installation of S2C.
Ligands+ are defined as including two subsets of 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 (which Jmol occasionally fails to identify as protein), excluding calcium (which Jmol incorrectly includes in "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.
  
  Very rarely, a ligand may fail to show as such, but show as a non-standard residue instead. An example is MYR1 in 1JSA. Jmol confuses it with GLY1 since neither has an insertion code (see bugs in Jmol).
- 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 GLY1:G in 4CPA, and A351:B in 1BKX.
  
  In rare cases, Jmol fails to recognize covalent bonds (see bugs in Jmol). This can cause a residue to appear not to be part of a chain (when in fact it is). An example is THR6 in 2SOC. See also anomalous atoms.
Protein, DNA, RNA, Carbohydrate: Definitions

DNA and RNA are defined within Jmol. No errors in these definitions have been noticed.

Protein is defined within Jmol, but the definition (in version 10.00.48) is flawed. Notably, calcium is included, and rarely, some standard amino acids fail to be included (examples). Therefore, FirstGlance defines protein as:
Using the Jmol-defined term "protein" includes some non-standard amino acids, as intended (see next section below).

Carbohydrate is defined in FirstGlance as follows:
(The above list is needed because, unlike "protein", "DNA", and "RNA", "carbohydrate" is not defined in Jmol.) Every group listed above was verified to be present in the Protein Data Bank. The above list was compiled from several sources, including personal communication with Thomas Luetteke (Thomas_L at MIT dot EDU), from which was derived a list verified to occur in the PDB by Jaime Prilusky, the Templates list at SWEET2. This list excludes some sulfated or phosphorylated sugars that occur in less than 10 PDB entries each. If you have suggestions for improving the list above, please send them (with sample PDB Id codes) to
Non-Standard Amino Acids and Nucleotides.

Initial View. Initially, non-standard residues are shown as crosses:
The crosses can be hidden, or the non-standard residues shown as balls and sticks, using controls under More Views...

Definitions. Standard amino acids and nucleotides are defined in the Protein Data Bank file format (PDB format), and have record type ATOM. These include:
- The 20 standard amino acids, plus ambiguous residue codes ASX, GLX, and undetermined UNK.
- Six standard nucleotides A, C, G, I, T, U plus UNK. (The PDB file format residue codes make no distinction between ribo- and deoxyribonucleotides.)
- Modified standard nucleotides designated +A, +C, +G, +I, +T, +U.
Backbone Traces. Non-standard amino acids and nucleotides, or the non-standard atoms within them, have record type HETATM. Regardless of whether the standard main-chain atoms within a residue are ATOM or HETATM, Jmol usually deems these residues "protein", "DNA", or "RNA" and includes them in backbone traces (a desirable feature that is unlike Chime).

Distinguishing Non-Standard Residues. When FirstGlance in Jmol is asked to highlight non-standard residues (with the checkboxes in the help panels for Ligands+ or More Views..), it does so by selecting "hetero and (protein, nucleic)".
- 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. Examples include GLY5 with PYL1005 in 1B07, phosphoserine (SER with PHO) and phosphothreonine (THR with PHO) in 1APM, and methylated ribonucleotides (e.g. +C1 with CH3) in 310D. This is unlikely to be correctable. In such cases, FirstGlance displays the non-standard portions of these residues as "Ligands+".
- Very rarely, non-amino acids are incorrectly displayed as non-standard amino acids, e.g. MYR1 in 1JSA. Correcting this category of problems is under consideration. More..
If you know of other cases not represented in the above examples, please email the PDB codes to
Advanced Uses of Find..

You can enter any atom expression, from Jmol's command language, into the Find.. slot. Examples:
1. RNA
2. MSE (the group name for selenomethionine, e.g. in 1K28)
3. 12-23 (all residues/groups with sequence numbers in this range)
4. 12-23:B (residues/groups in chain B with sequence numbers in this range)
Note that "atoms with halos" (from Find..) can be designated as a target for the Contacts.. displays (see the checkbox for this purpose in Contacts..). That is, you can visualize atoms non-covalently interacting with the "atoms with halos". Thus, Find.. can be used to select target atoms that are problematic to select with the target selection options in the Contacts.. interface.
FAQ* for Target Selection for Contacts.. (*FAQ = Frequently Asked Questions)
1. What are "atoms with halos"? Use the Find.. link in the upper left panel to apply halos to atoms. 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 More Views.. or Ligands+.) 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).
  - 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 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...
The mechanism used to select unnamed chains is detailed in Technical Information.
Contacting Atoms: Definitions

The Contacts.. dialog in FirstGlance shows atoms likely to be noncovalently (or covalently) bonded to any target set of atoms that you select. Such atoms are deemed "contacts", and are shown as spheres (either of van der Waals radii, or of smaller radii in "ball and stick" rendering). "Contacting" atoms are determined solely by distance from the target, using the following criteria. Suggestions for improving the following criteria are welcome (see feedback address at the bottom of this document).

Jmol has a built-in mechanism for displaying hydrogen bonds as broken lines between DNA base pairs, and in protein backbone secondary structure. This mechanism is currently rudimentary, and because it shows only a small subset of the hydrogen bonds actually present, it is not used by FirstGlance. (For details, see the hbonds command in the Jmol Reference Manual.) FirstGlance shows only the proximal atom pairs, leaving it to the viewer to judge whether a non-covalent bond actually exists between them.
- 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 More Views.., Quality, All-atom contact analysis). 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 (see Model Quality under More Views..).
  - 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 4.5 Å 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 example of hydrophobic interactions: The two chains of 1D66 contact each other forming a small, buried, hydrophobic core.
- 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 salt bridges in FirstGlance: (i) Contacts.. shows them between a target you select and the remainder of the model; (ii) More Views.. enables you to find them throughout the model.
  - Example: Each chain in 2HHD has one salt bridge in each direction between chains A and C.
- Cation-pi orbital 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 orbital 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) More Views.. enables you to find them throughout the model.
  - 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. This is a bug that is difficult to fix. 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. Protein Explorer's Advanced Explorer provides a means to visualize these.
    - 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, 2006, which include the following:
    The following elements did not occur in the Protein Data Bank in April, 2006. Sulfurs interacting with these would not be displayed.
    - bismuth, francium
    - Alkaline earths: radium
    - Transition metals: scandium, titanium, niobium, hafnium
    - Lanthanides: hafnium, 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.
  - 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).
The above rules can undoubtedly be improved. Also, since not all possible interactions have been tested, there may be errors in the implementation of these rules. Please send your suggestions to the feedback address (at the bottom of this document).
Hydrogen in Macromolecular Models

Hydrogen is often absent in crystallographic models, because it is usually not resolved by X-ray diffraction. In contrast, hydrogen is typically present in NMR results. In some crystallographic models, hydrogens have been added by molecular modeling, either to polar atoms only, or to all atoms.
Here is More about Hydrogen.
- 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.
Contacts: Labels

A label is shown for each amino acid or nucleotide (including non-standard residues) that contains any contacting atoms. (Labels are not shown for contacting ligands or solvent. Click on these to identify them.) Labels are in this format: PRO 36:D Labels use 3-letter amino acid abbreviations. The letter following a colon (":D" in the example above) identifies the chain to which the residue belongs. Labels are attached to the alpha carbon atoms of amino acids, or the phosphorus atoms of nucleotides. If these atoms are among the contacting atoms (see above), the label is connected to its atom with a broken line (but a high zoom level is needed to ensure that the line connects to the correct atom). If not, the broken line points to the invisible alpha carbon or phosphorus.
Anomalous Atoms (Controls are under More Views..)

Definition. Atoms that are not recognized by Jmol as being one of: protein, nucleic acid, or "hetero".

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.

Problem. FirstGlance will often fail to display anomalous atoms appropriately. Some anomalous atoms will be invisible in all views except Vines (with details on).

Solution. In order to avoid leaving anomalous atoms invisible, they are initially always shown as dot surfaces of van der Waals radii (see snapshot at right). The colors of the dots vary depending on the view. These dots are easily distinguished from halos because they are less dense, are arranged in a spherical pattern instead of a flat ring, and are usually not yellow. In order to identify the anomalous atoms, go to More Views.., where you can display them as spheres. This enables you to click on them for identification.

More Views.. also has an option to hide the dots for anomalous atoms.

Examples:
- The main chain oxygen (.O) is missing from GLY5 in 1B07, and MET79:M in 1UC5.
- THR918 in 1H3O, and ALA333:C in 1PRC lack all atoms except the peptide-bonded nitrogen.
  
  Errors in PDB file format.
- FOR0:H in 1PRC should be HETATM but is ATOM.
  
  Possible errors in interpretation by Jmol (version 10.2.0). (See Bugs in Jmol. No main chain atoms appear to be missing.)
- 1GRH has only two residues, CYS (ATOM) and HEC (HETATM). Jmol fails to recognize the CYS as protein, and fails to connect its main chain atoms.
- In some entries containing D amino acids, Jmol fails to recognize some standard L amino acids as protein:
  - All standard amino acids in 2SOC. Jmol fails to connect the anomalous atoms. The sequence of this octapeptide (from SEQRES) is DPN CYS PHE DTR LYS THR CYS THO. Because THR is (erroneously) not connected at either end, FirstGlance deems it to be Ligand+.
  - VAL1, ILE1^A, GLY2, ALA3 in 1AL4. Note that both VAL1 and ILE1^A (the ^A represents an insertion code, column 27 in the ATOM record) occupy the same position in the chain sequence. This represents sequence microheterogeneity in the protein that was crystallized.
Measuring Distances and Angles

To measure the distance between two atoms, double click on the first atom. Now, as you touch other atoms, the distances will be shown on a red line connecting the atoms (except in Mac Firefox). Double click on a second atom to fix the distance report.

If you wish to cancel without fixing a distance report, simply move the mouse outside of the Jmol rectangle. If you wish to remove one already fixed report, double click on each of those two atoms again. If you wish to remove all distance and angle reports, click on the Hide link (in Contacts Shown), or click on More Views.., then on the link Hide distances and angles. (The Jmol command to do this is "monitors off".)

To measure an angle, double click on the first atom, then single click on the second. As you touch additional atoms, the angle will be displayed on a red line. Double click the third atom to fix the angle report.

To measure a torsion (dihedral) angle, follow the same kind of procedure, except four atoms are needed.
Firefox Browser

Firefox (getfirefox.com) is an excellent, popular, free, open-source web browser in the Gecko family.

Windows: Firefox 1.0 and 1.5 work well with FirstGlance in Jmol. On Windows, Firefox (and other browsers) do not require browser-specific java updates, but use the system-wide java.

Mac OSX: Safari is preferable to Firefox on Macs, although Firefox 1.5 is acceptable. It is imperfect in that when clicking on an atom to identify or center it, one often has to click twice before the correct response occurs. Also, when measuring distances or angles, the result may not be displayed (in pink) when touching the final atom; or if it is, the line may not be cancelled when the mouse is moved out of the Jmol rectangle. Regardless, the result is displayed after double-clicking the final atom.
linux: Firefox appears to support FirstGlance in Jmol in Knoppix, but we have inadequate information for linux.

See also Safari and Compatible Browsers.
Safari Browser

Safari is a web browser included in the Apple Macintosh OSX computer operating system. It works well with FirstGlance in Jmol. However, in late 2005, the following problem occurs when using Safari under OS 10.3.9: Sometimes the links and buttons that control the molecular view fail to work. Simply quit and restart Safari to cure this problem, or upgrade to OSX 10.4 Tiger to avoid this problem entirely.
Another minor anomaly in Safari in OS 10.3.9 is that "hover" reports of atom identity do not appear. (They do appear in OS 10.4.) However, in all versions of Safari/OSX, clicking an atom correctly produces an identity report in the lower left of the applet rectangle.

See also Mac Firefox and Compatible Browsers.
Uploading PDB Files

Security. Your data file (which must be in PDB format, but can have any filename type suffix) is transferred through the Internet unencrypted, and stored temporarily on the server at Bioinformatics and Biological Computing of the Weizmann Institute of Science in Rehovot, Israel. It is then re-transferred through the Internet to the Jmol applet in your web browser. A sophisticated spy could capture your data. Institutions needing a secure method to upload proprietary data for display in FirstGlance in Jmol may install FirstGlance in Jmol within their secure intranet. Feel free to contact with any questions.

Method. Jaime Prilusky kindly provided a CGI program that accepts uploaded PDB files. You can put an upload slot to this program on your own web page by inserting the following HTML:
```
<form method='post' enctype='multipart/form-data'
    action='http://bip.weizmann.ac.il/oca-bin/fgij'>
  Upload a PDB file of your own:
    <br><small>
    Caution: uploading a PDB file may <b>disclose your data</b> to others.
    </small><br>
  <input type='file' name='file' size='50'>
  <input type='submit' value='View in FirstGlance'>
</form>
```

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