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 OS X only, you often have to click twice (or four times?)
before the report is produced. Safari is better!)
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.
Atoms are identified using PDB file format nomenclature, as follows:
|
CA = Carbon, Alpha (1st) CB = Carbon, Beta (2nd) CG, OG = Carbon/Oxygen, Gamma (3rd) CD = Carbon, Delta (4th) CE, NE, OE = Carbon/Nitrogen/Oxygen, Epsilon (5th) NZ = Nitrogen, Zeta (6th) NH = Nitrogen, Eta (7th) |
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.
In January, 2006, the hover report does not work in Safari under Mac OS X 10.3.9, but does under Mac OS X 10.4 ("Tiger") and 10.5 ("Leopard"). The clicking report works in both.
Most molecules will have none of these labels when displayed in FirstGlance in Jmol. Some molecules will have one or more of these kinds of labels.
- X marks non-standard residues.
- S- marks incomplete Sidechains.
- ? marks anomalous atoms.
These labels or marks are shown by default, but can be hidden by
unchecking the checkbox Labels: Show at the bottom of the
upper left panel (below New Session).
By default, labels behind other atoms are hidden. To make sure you can see all labels, check the checkbox Labels: Front at the bottom of the upper left panel (below New Session).
Check ID to add identifications to the labels for all atoms marked X, S-, or ?.
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 of amino acids or nucleotides can be viewed by any of these means:
- Key Resources link, then PDB. There, the Sequence tab near the top. These are annotated, one-letter sequences with links to other resources. Residues with no coordinates ("gaps" in the model) lack the 3 lines above and below the sequence. It is hard to be sure you have seen all the gap here, so we recommend the S2C method below for finding all gaps quickly.
- Key Resources link, then OCA. There, look below in the Sequence-derived information section for one-letter sequences in FASTA format plus links to other resources.
- available at OCA (see previous paragraph). At OCA, use the link SEQRES to COORDINATES in the first blue section, Data Retrieval.
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, 535into 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.
- 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.
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 10.9.x) is flawed. 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
View Options. Initially, non-standard residues are labeled X. These labels can be controlled with the labels checkboxes. Also, the non-standard residues can be 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.
- 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.
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. 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.)
Sidechain atoms may be missing from some residues. Residues with missing sidechain atoms are marked S- (see Labels). Typically, the atoms farthest from the alpha carbon may be omitted from the model due to local disorder (low resolution) in the electron density map. Examples include 1BL8 and 1APM.
In the Charge.. display, there is an option to color charged atoms only. Since these are at the ends of sidechains, farthest from the main chain alpha-carbon atoms, they are sometimes missing, and cannot be colored. Light colors are applied to all atoms present in such residues (in addition to S- labels) are used to indicate where this occurs.
|
| Appearance of a protein model that contains only alpha-carbon atoms (1A1D). |
Methods: In each standard residue, one or two atoms farthest from the alpha carbon (or phosphorus atom in nucleotides) are checked. If any of these atoms are missing, the alpha carbon (or phosphorus) is labeled S-. The list of atoms checked is in this spreadsheet (MS Excel format): sidechain_termini.xls. The script that selects residues with incomplete sidechains is in the file scripts.js, in makeDefineIncompleteSidechainsSpt().
Atoms missing in non-standard residues or ligands will not be reported.
If a standard residue contains some atoms, but lacks the alpha carbon or phosphorus atom, the S- label will fail to be displayed.
You can enter any atom expression, from Jmol's command language, into the Find.. slot. Examples:
- RNA
- G, C (guanidylate and cytidylate in either DNA or RNA)
- DA, DT (adenylate and thymidylate in DNA; see standard residues)
- (G,C) and RNA (guanylate and cytidylate in RNA)
- MSE (the group name for selenomethionine, e.g. in 1K28)
- 12-23 (all residues/groups with sequence numbers in this range)
- 12-23:B (residues/groups in chain B with sequence numbers in this range)
- 12-23 and ~protein (excludes non-protein, such as water or DNA)
- 12-23 and ~nucleic (excludes non-nucleic, such as water or protein)
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.
The Probable Quaternary Structure (PQS) server of the European Bioinformatics Institute attempts to predict whether specific oligomers were present in a crystal structure. If so, it generates models of them that you can explore in FirstGlance in Jmol. If the published PDB file (the asymmetric unit) contains more than one copy of the monomer or specific oligomer, PQS generates a model of a single monomer or specific oligomer (biological unit). A more detailed explanation with examples is the Introduction to PQS (within Protein Explorer).
After you see the PQS report, follow the instructions below to see oligomers or monomors prepared by PQS. To see the PQS report, enter the PDB code of interest and click Go:
- At the PQS report page, right click (Mac: Ctrl-Click) on the RasMol link to the .mmol file (NOT the red button!) that you wish to display, and Copy Link.
- At the main page of firstglance.jmol.org, click on enter a molecule's URL.
- Paste the copied link into the slot, and click the Submit button.
The methods of PQS apply only to crystal structures. If you submit a structure determined by NMR, you will be redirected to the OLDERADO server, which determines the model most representative of the average of the models in the published ensemble.
You may also wish to consult a newer server by the same group, PISA.
- 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).
- 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.
- If there are only a few, change the selection mode to
Residues/Groups and click on each of them.
- 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.
- If there are only a few, change the selection mode to
Residues/Groups and click on each of them.
- 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:
- 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.
- 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.
- 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.
- 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...
The mechanism used to select unnamed chains is detailed in Technical Information.
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 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.
- 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).
- Simple example of hydrogen bonds:
Either protein chain in 1D66 recognizes the DNA sequence
CGG through hydrogen bonds.
- Water and water bridges.
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.
Water bridge in 1D66 between the sidechain nitrogen of Arg 46
(chain B)
and the phosphate in Cytosine 13 (chain D).
Furthermore, water bridges can be shown separately (a subset of hydrogen bonds involving water). Each bridge includes at least these three atoms:- A target oxygen or nitrogen within 3.5 Å of a non-target water oxygen.
- The bridging non-target water oxygen.
- 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 protein 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. Salt bridges where one or both partners is not a standard amino acid are not shown in these views (but can be shown using Advanced Explorer in Protein Explorer.)- 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. Cation-pi interactions where one or both partners is not a standard amino acid are not shown in these views (but can be shown using Advanced Explorer in Protein Explorer.)- 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.
-
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.
- 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.
- Metal and miscellaneous bonds
include three categories of distance-based atom pairs.
- 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:
- bismuth, francium
- Alkaline earths: radium
- Transition metals: scandium, titanium, niobium, hafnium
- Lanthanides: hafnium, neodymium, promethium, dysprosium, thulium
- Actinides: actinium, thorium, protactinium, neptunium, plutonium, americium
- 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.
- 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.
- 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).
- 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:
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.
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:
Anomalous atoms were a problem in version 1.0 of FirstGlance. Since version 1.0 was released in 2007, improvements in Jmol, and remediations of the PDB have largely eliminated the problem of anomalous atoms.
Definition. Atoms that are not recognized by Jmol as being one of: protein, nucleic acid, or "hetero".
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.
Problem. FirstGlance will often fail to display
anomalous atoms appropriately. Some anomalous atoms could 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), and labeled ?. These labels can be hidden, brought to the front, or expanded into full identifications with the Labels Checkboxes.
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.
More Views.. has an option to hide the dots for anomalous atoms, without hiding the labels for missing sidechains and non-standard residues.
Example:
- THR918 in 1H3O, and ALA333:C in 1PRC lack all atoms except the peptide-bonded nitrogen. In February, 2010, Jmol 11.8.19 fails to recognize these ATOM nitrogens as protein atoms.
Missing main chain atoms. This could result from lack of electron density, or simply from errors in published PDB files.
The above example is the only remaining case that I know about in February, 2010. Below, for your entertainment, are some formerly troublesome cases that FirstGlance and Jmol now handle correctly.
Odd PDB files now handled correctly:
- The main chain oxygen (.O) is missing from
GLY5 in
1B07,
and MET79:M in
1UC5.
- 1GRH has only two residues, CYS and EOH (ethanol). Formerly, CYS atoms were ATOM, and EOH was called HEC with HETATM. After remediation, the CYS is also HETATM. FirstGlance properly treats both residues 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.
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 (getfirefox.com) is an excellent, popular, free, open-source web browser in the Gecko family.
Windows: Firefox 1.0 and later versions 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 OS X: Safari is preferable to Firefox on Macs, although Firefox 1.5 or later is acceptable. It is imperfect in that when clicking on an atom to identify or center it, one often has to click twice (or four times) before the correct response occurs -- or you may be unable to get the correct response. This remains true in Firefox 3.5. When measuring distances or angles, click four times on the first atom; the result may not be displayed (in pink) when touching the final atom; or you may be unable to fix the report by clicking 2-4 times on the second atom.
Another annoyance in Firefox is that the molecule usually disappears briefly (Jmol goes blank) when the view is changed. This does not happen in Safari.
Firefox 1.0 does not support FirstGlance in Jmol. Mac OS X users should use Firefox 1.5 or later, which supports FirstGlance in Jmol in OS 10.3.9 ("Panther"), OS 10.4 ("Tiger"), and 10.5 ("Leopard")..
linux: Firefox appears to support FirstGlance in Jmol in Knoppix, but we have inadequate information for linux.
See also Safari and Compatible Browsers.
Safari is a web browser included in the Apple Macintosh OS X computer operating system. It works well with FirstGlance in Jmol. Problem with OS 10.3.9 only: 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 OS X 10.4 or later to avoid this problem entirely.
-
The problem results when other java-using websites are visited before
FirstGlance in Jmol in the same Safari session. The problem
appears to reflect a bug in Apple's java. It has been
reported to them.
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 and later.) However, in all versions of Safari/OS X, clicking an atom correctly produces an identity report in the lower left of the applet rectangle.
See also Mac Firefox and Compatible Browsers.
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 OS X, 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.
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 a 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>