FirstGlance in Jmol
• Overview & Design Goals (11/2020 with FirstGlance version 3.0: Biological Assemblies are now the default, even for very large structures such as virus capsids.)
• Protein Crosslinks: Five kinds of covalent crosslinks between protein chains are detected automatically. Examining the electron density map helps with validation. (8/2024 with FirstGlance version 4.3)
  
  Other Subjects
• Ramachandran Principle: Protein Atomic Clashes vs. Phi & Psi (>80,000 hits)
• Antibody Structure & Function
• Major Histocompatibility Protein Structure & Function
• Pockets & Cavities Using Pseudoatoms in Proteins: PACUPP: Demonstration of a free, Jmol-based software package with illustrations.

1. ID Code: As a standard 4-character wwPDB accession code such as 1ijw (more examples). The ID code can be entered by hand into the PDB code slot at the front door of FirstGlance, or specified in a link or URL. Example: firstglance.jmol.org/fg.htm?mol=1ijw.
   
   
2. URL: When the PDB file is available online, its URL (internet address) can be pasted in to the URL slot at the front door of FirstGlance (see snapshot), or specified in a link (instructions). Example:
   firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/atlas/pdb/dna_b_form.pdb.gz.
   
   
3. Upload: Any file in PDB Format that is available on your local computer can be uploaded to FirstGlance from its front door (see snapshot).

• AlphaFold3 Server accommodates multiple protein and/or nucleic acid chains, a limited set of ligands and metal ions, and an extensive range of post-translational amino acid modifications and chemical modifications of nucleotides. AlphaFold3 assigns chain IDs to complexes differently than does wwPDB to empirical models. Predicted models are easily converted to PDB format for compatibility with FirstGlance, as they are provided only in mmCIF format. Predicted models lack job descriptions, so, beginning summer 2025, FirstGlance offers to identify chains from their sequences (see snapshot at right).
  
  Examples of AlphaFold3 Server Predictions:
  • Protein tetramer with heme, predicted May 2025: Amphibian Hemoglobin. Four HEM + two alpha-like and two beta-like chains of hemoglobin from the legless (wormlike) African amphibian Geotrypetes seraphini. When predicted, the closest sequences for empirically-determined structures in the wwPDB were ≤53% sequence identical avian hemoglobins.
  • Protein, 1 chain, predicted November 2024: Human ubiquitin protein ligase E3A (partially untemplated, see analysis vs. 8jrp).
  • Protein-Glycan-Ion example provided by the server, a prediction of 7BBV: Pectate lyase B. Compare with empirical "ground truth" structure 7bbv and see superposition.
  • Protein-DNA-Ion example provided by the server, a prediction of 7RCE: Synthetic constructs. The predicted model fills in 85 incomplete sidechains and a 4-residue missing loop, restoring 51 charges that are missing in the 2.4 Å X-ray empirical model. Thus, AlphaFold models are recommended to be analyzed alongside empirical models since the former have complete charge distributions and shapes. Compare with empirical "ground truth" structure 7rce.
  • Protein-tRNA-Ion example provided by the server, a prediction of 8AW3: tRNA deaminase. Compare with empirical "ground truth" structure 8aw3.
• ColabFold (using AlphaFold2 + AlphaFold2-multimer) predicts multiple protein chain complexes. Example:
  • Protein, 4 chains (alpha₂ beta₂), predicted May, 2025: Hemoglobin of loggerhead sea turtle (Caretta caretta) without hemes. When submitted in May, 2025, there were no empirical hemoglobin structures for this taxon in the wwPDB. The closest empirical structure sequence was 74% identical (3AT5, hemoglobin of side-necked turtle, Podocnemis unfilis).
• The AlphaFold Database offers ready-made predictions of single-chain protein-only structures without ligands. Examples:
  • Iron phytosiderophore transporter of Zea Mays (Q9AY27). Unlike predictions from the AlphaFold Server and ColabFold, AlphaFold Database predictions have a header section, enabling FirstGlance to recognize them automatically as AlphaFold predictions.
• RoseTTAFold (an option at the Robetta Server) predicted PDB files have a header section, enabling FirstGlance to recognize them automatically and color them initially by estimated error. Example -- the protein can be easily identified from the amino acid sequence in the predicted model (see snapshot above).

• AlphaFold and ColabFold estimate per-residue confidence (pLDDT) with values ranging from 0 to 100 placed in the temperature field of the ATOM records in PDB files. FirstGlance applies an estimated confidence color scheme based on documentation at AlphaFold (look for "How confident shoule I be ..."). See examples above.
  
  
• RoseTTAFold results are colored with an arbitrary scheme by FirstGlance that is the same for all models. See examples above. RoseTTAFold puts an estimated Å error in the temperature field, ranging from 0.0 to 1.0 for very high confidence to values > 25 for very low confidence. At the Robetta Server, colors applied are not in spectral order: blue (highest confidence), purple, red, orange, and yellow (lowest confidence). Cutoff ranges for each color vary from model to model. For example the estimated highest error colored blue is ~ 1.5 for some models, but rises to ~4 in other cases. Similarly, the lowest estimated error value colored yellow is ~ 7 for some cases, but rises to >20 for other cases. Nevertheless, some models with low overall estimated confidence have no blue or purple regions. No explanation of this color scheme is evident, and these variations do not appear to be explained by the overall estimated confidence reported for each model. (Observations made in May, 2025.)

If the published model available from the wwPDB is what you want, there is no reason to get into the complications of using a ".pdb" file; simply specify the wwPDB 4-character accession code.

• FirstGlance will initially display the coordinates in the file, which typically represent the asymmetric unit. Because FirstGlance does not know the size of the model before loading it, it cannot do automatic simplification. Large models (30,000 - 99,999 atoms) will be slow to load and sluggish to manipulate.
  
  
• If REMARK 350 is present in the .pdb file, and if at least a minimal header section is present (keep reading), then the Molecule Information Tab will offer a link Functional Assemblies (Biological Units) are specified!. Following that link will display a clickable list of Biological Units, each of which can be displayed in a separate browser tab. (The free program Chimera can generate REMARK 350 records in PDB format.)
  
  Minimal Header Section: In addtion to the ATOM & HETATM records and REMARK 350 (REMARK 300 is not required), at a bare minimum, the following lines would need to be added by hand to the top of the PDB file in order for FirstGlance to process REMARK 350 correctly. Be sure to use a Plain Text Editor!

  COMPND    MOL_ID: 1;                                                            
  COMPND   2 MOLECULE: PROTEIN;                                            
  COMPND   3 CHAIN: A, B;                                                         
  EXPDTA    ELECTRON MICROSCOPY
  REVDAT   1                                                                       
  REMARK   3 REFINEMENT.                                                          
  

  • There must be a block of 3 COMPND lines for each group of sequence-identical chains. In the example above, chain A has the same sequence as chain B. You must put the actual single-character chain IDs in the COMPND 3 records.
  • EXPDTA specifies the method that FirstGlance will display, and it will affect the behavior of FirstGlance. Standard EXPDTA methods are X-RAY DIFFRACTION, ELECTRON MICROSCOPY, or SOLUTION NMR.
  • The contents of the REVDAT and REMARK 3 lines don't matter, but if these lines are missing, FirstGlance will not process REMARK 350 properly.
    
    
  • Example: 4uft is a helical Measles virus protein nucleocapsid containing RNA. There are 2 sequences in the asymmetric unit, and 78 chains in the model specified by REMARK 350. A copy of the published PDB file has been stripped down to a bare minimum and bundled with FirstGlance for testing/demonstration purposes.
    • Display 4uft from the wwPDB in FirstGlance. Because FirstGlance can get the model size from the wwPDB, it can automatically decide the level of simplification needed BEFORE loading the PDB file.
    • Show contents of the minimal 4uft PDB file.
    • Display minimal 4uft in FirstGlance: Initially the asymmetric unit will be displayed.
      • Look for the link Functional Assemblies (Biological Units) in the Molecule Information Tab. When you click it, all Biological Units specified in REMARK 350 will be listed. When you click on Biological Unit 1, a new tab will open showing the simplified 78-chain assembly.
      • Because most of the header section of the PDB file was deleted, the Molecule Information Tab reports PDB File Does Not Say for Resolution, Reliability (Rfree), Missing Residues, and Ligands & Non-Standard Residues.
      • To see the RNA: Views tab, Composition, then depress the Slab button. Or Views tab: Solid. Focus box: Hide, check Protein.
  
  
• When displaying Biological Units, FirstGlance will automatically simplify the model as needed for good performance. (This is possible because the initial display of the asymmetric unit passes the sizes of Biological Units to new browser tabs, enabling FirstGlance to make simplification decisions BEFORE loading the .pdb file.)
  
  
• You can construct a link (or URL) that will display a Biological Unit initially by including &bu=N in the URL, where N is the number of the desired Biological Unit. For large biological units (>25,000 non-H atoms), simplification to backbone atoms should also be specified in the URL. If you don't do this, loading may take a long time, or for huge biological units, the browser may simply freeze. Your goal should be to keep the number of backbone atoms <25,000 for smooth performance. &bbonly=1 loads all backbone atoms, while &bbonly=N loads the subset of every Nth backbone atom. See query parameters for more details.
  
  
• Examples: Below is explained how to extract residues within 20 Å of the mRNA, tRNA, and nascent peptide (chains A, B and C respectively) in PDB format from the mmCIF ribosome model 5np6.
  • Display 5np6-within20-ABC.pdb. (This .pdb file is bundled with FirstGlance, so can also be displayed this way.)
    
    
  • This example has only 24,987 non-H atoms, so does not require simplification. But as an example, here is a link simplifying it to backbone atoms only (alpha carbons plus nucleic phosphorus atoms) by adding &bbonly=1 as explained in query parameters: 5np6-within20-ABC.pdb backbone atoms only.

• ConSurf: Evolutionary conservation patterns are available in PDB files prepared for FirstGlance by the ConSurf Server, or obtained from the ConSurf Database. ConSurf-processed PDB files can be analyzed in FirstGlance by clicking the link to FirstGlance at the ConSurf results page, or by downloading the PDB files containing Consurf results for FirstGlance, and then uploading them to FirstGlance. See also Simplification of ConSurf Results, and how to use ConSurf.
  
  Published PDB files processed by ConSurf should retain "consurf" in their filenames for optimal handling by FirstGlance (especially when the .pdb file is on a server remote from the FirstGlance server). The filename should begin with the PDB identification code.
  Examples:
  • 7mgp_A_consurf_firstglance.pdb: Biological Unit 1 is a hexamer of the asymmetric unit. Biological Unit 1 is shown initially.
  • 2vaa_consurf1149872322_pipe.pdb.gz: No biological units are specified.
  When ConSurf .pdb files are uploaded to FirstGlance, the filename becomes "data.pdb". Nevertheless, FirstGlance will recognize these as ConSurf files and process them appropriately, including initial display of Biological Unit 1.

  (Technical: FirstGlance version 4.1 "peeks" into files with names ending ".pdb" [see dotPDB] that are on the same server as FirstGlance [all uploaded files] to find out whether they are ConSurf files. This is done before loading the PDB file. See peekConsurf() in moldoc.js, and ajaxThenJSmol() in scripts.js.)

  Unpublished models: ConSurf analysis: An unpublished model can be uploaded to the ConSurf server for analysis. The PDB file produced by ConSurf can then be uploaded to FirstGlance. FirstGlance will color the model by evolutionary conservation regardless of whether the filename contains "consurf" (see Technical note above).
  
  Biological Units: If the PDB file contains REMARK 350 (REMARK 300 is not required) specifying biological units, but no other standard PDB file format header section, FirstGlance will initially display the model "as is" (asymmetric unit). Next, Go to the Firstglance Control Panel. If Biological Units are specified in REMARK 350, the Molecule Information Tab in FirstGlance will offer a link Functional Assemblies (Biological Units) are specified!. Clicking it will offer links to display each Biological Unit.
  
  Examples:
  • Show text contents of file conservation.pdb. This ConSurf file has REMARK 350 plus a minimal header section.
  • Display file conservation.pdb in FirstGlance. Click Functional Assemblies in the Molecule Information Tab to get Biological Unit 1. Click Act on all 6 sequence-identical chains by the flashing red arrow to color the entire biological unit by conservation.
  • Display file model_consurf.pdb in FirstGlance. The contents of this file are identical to the contents of conservation.pdb. But because "consurf" is in the filename, FirstGlance displays Biological Unit 1 initially. Note that if this file were uploaded to FirstGlance, because its filename becomes "data.pdb", it would behave the same as conservation.pdb.
  • Show text contents of file conservation-noheader.pdb. This ConSurf file has REMARK 350 but NO header section.
  • Display file conservation-noheader.pdb in FirstGlance. This ConSurf file has no header section. Therefore, the REMARK 350 in this file is ignored by FirstGlance, and Functional Assemblies will not be offered.
  
  
• AlphaFold Database: Models predicted by the AlphaFold Database. See explanation at AlphaFold in Proteopedia. Example: Iron phytosiderophore transporter of Zea Mays (Q9AY27). See also more examples, including AlphaFold predictions pre-processed by ConSurf.
  
  
• RoseTTAFold: Models predicted by the RoseTTAFold Server. Example: UniProt W9JUF2, Fusarium oxysporum protein of unknown function. See also ConSurf analysis of this example.
  
  
• Swiss-Model: Homology models generated by Swiss-Model. Example: Swiss-Model of human enoloase.
  
  
• Orientations of Proteins in Membranes (OPM): PDB files processed by the OPM Server. Pseudoatoms mark the predicted boundaries of the lipid bilayer. OPM files may include the original PDB header with REMARK 350 specifying biological units. However, FirstGlance does not display the biological assembly, since is not useful for OPM results. (Because the filenames of OPM-processed models do not indicate their origins, FirstGlance initially loads the PDB file as the default biological unit 1, then recognizes its origin from the contents, and then restarts to load the asymmetric unit rather than biological unit 1.) Example: 4fz0-opm.pdb.
  
  Additional code was implemented to handle OPM PDB files because they do not obey wwPDB rules:
  1. For some models, all water chain IDs are changed to W (example: 1foe-opm.pdb). In other models, water and ligand chain IDs are changed from their associated protein to new/arbitrary chain IDs (example: 1r3j-opm.pdb).
  2. Sometimes N & O atoms representing the lipid-water boundaries, group name DUM (for dummy) have no chain ID (example: 1foe-opm.pdb). In other cases, a chain ID is assigned (example: 4fix-opm.pdb.gz).
  (Technical: See pdbIsOPM, removeBlankOPMChainID() and removeOPMWaterChainID().)
  
  
• Unpublished models with REMARK 350 symmetry operations to construct a Biological Unit/Functional Assembly. Provided you can generate REMARK 350, you don’t need much more of a header section. See instructions above for a minimal header.
  
  
• No Header Section: PDB files generated by various software systems or edited by hand may have no header section, or a non-standard header section. Examples:
  
  
  • ColabFold: Predictions from amino acid sequences submitted to ColabFold (AlphaFold2-multimer) have no header section whatsoever. When a PDB Format file has no header section, FirstGlance asks whether it is an AlphaFold prediction. Examples:
    • 2025 4-chain ColabFold prediction: Sequences of 2 alpha chains (Q10732) and 2 beta chains (Q10733) of loggerhead sea turtle (Caretta caretta) hemoglobin were submitted, giving this predicted tetramer. When submitted in May, 2025, there were no empirical hemoglobin structures for this taxon in the wwPDB. The closet empirical structure sequence was 74% identical (3AT5, hemoglobin of side-necked turtle, Podocnemis unfilis).
    • 2021 single chain AlphaFold Colab prediction for UniProt Q709E2. Also available pre-processed by ConSurf.
    
    
    
  • XYZ Format: See XYZ Format.
    
    
  • Saved from Jmol: PDB files written by the Jmol.jar Java stand-alone application have no header section. Jmol writes only the currently selected atoms, so it provides a convenient way to save a subset of atoms into a PDB file. For example, consider 5np6, a 3.6 Å EM model of a 2.2 MDa 70S E. coli ribosome. It has 146,883 non-hydrogen atoms (>99,999), so is too large for PDB format. It has 57 chains (< 62, the limit for PDB format). Chain A is mRNA, chain B is tRNA, and chain C is the nascent peptide (topoisomerase). Using Jmol.jar, the following commands save only those three chains into a new PDB format file:

    load =5np6.cif
    select on chain=A or chain=B or chain=C
    write "5np6-chains-ABC.pdb"
    

    There is no header section in the resulting PDB file: Display 5np6-chains-ABC.pdb in FirstGlance. Jmol writes CONECT records for most covalent bonds. These are voluminous and unnecessary, and confuse some versions of Jmol. They should be deleted with a plain text editor.
    
    Here is a nice demonstration of the initially surprising discovery that the peptidyl-transferase is a ribozyme, not a protein enzyme. (See 2009 under Nobel Prizes for 3D Molecular Structure, and Polacek & Mankin, 2005 -- full text.) Save the mRNA, tRNA and nascent peptide (chains A, B, and C) along with those residues having any atom within 20.0 Å of any atom in the 3 chains A, B, or C.

    load =5np6.cif
    select on within(group, within(20.0, (:A,:B,:C))) # ":A" is a synonym for "chain=A".
    write 5np6-within20-ABC.pdb # 24,987 atoms.
    

    When displayed in FirstGlance (after deleting the CONECT records), residues that have been separated from others in their chain (by the 20 Å cutoff) behave as "ligands+" in FirstGlance. The 16S rRNA is chain D, and the 23S rRNA is chain Y. Use "Find.." in FirstGlance to find chain=Y (yellow halos). Then use "Hide.." to hide "Atoms with Halos". Center the junction between the tRNA and the nascent peptide. Notice that the ribosomal amino acid closest to this junction (Arg81 of chain k, 50S ribosomal protein L16) is ~14 Å away from Gly46 of nascent peptide chain C, too far away to be the peptidyl-transferase. (View as Sticks, checking "more detail" to make distance measurements. Click Distances/Angles in the Tools tab for how to measure.)
    
    What is touching this junction? In the Tools tab, click Contacts & Non-Covalent Interactions. Select Residues/Groups. Click on the tRNA residue and the nascent peptide residue that touch each other (the "junction"). Click Show atoms contacting target. Exploring the result, you will find that 6 rRNA residues appear to be interacting non-covalently with the junction residues.

PDB Identification Codes
• abcd, 0abc, 1abcd, 1a@b: Invalid PDB identification codes.
• 1abc Entry does not exist: this PDB ID code is not assigned to any entry.
• 2cx2 WDRN, withdrawn by its depositors before being released.
• 1vsz OBS, obsolete and superseded.
• Status HPUB or HOLD: search for test entries by status at rcsb.org/pages/unreleased.
• 5np6 (huge), 8rox (5-character ligand ID): Not available in PDB format (only mmCIF format). In April, 2024, 2.3% of entries in the wwPDB are not available in the PDB format.
Filenames ending ".pdb"
• Without a server address, FirstGlance expects such files to be included in its subdirectory localPDBFiles. An example of a file included there is firstglance.jmol.org/localPDBFiles/RoseTTaFold-W9JUF2.pdb.
• RoseTTaFold-W9JUFF.pdb File not available within FirstGlance*. Compare with RoseTTaFold-W9JUF2.pdb.
Internet Addresses (URLs)
• molviz.org/models/nosuch.pdb Bad URL.
XYZ Files
• M24L48-single-polyhedron.pdb.
mmCIF Files
• 3j3y HIV capsid, available only in mmCIF format.
• 1ijw.cif mmCIF requested, despite PDB format being available.
• molviz.org/models/1ijw.pdb This filename ends in ".pdb" but its contents are actually in mmCIF format. It is mis-named. Check it out!

• S— marks incomplete Sidechains or nucleotides*. The following terms can be entered into the Find.. dialog (in the Focus Box):
  • ~incomplete_sidechain_residues (all atoms present in amino acids with incomplete or missing sidechains or nucleotides with incomplete or missing bases)
  • ~incomplete_sidechains (only the alpha carbons or nucleotide C5' atoms in amino acids with incomplete or missing sidechains or nucleotides with incomplete or missing bases)
  • ~incomplete_stdaa_sidechain_alphacarbons (only the alpha carbons of standard amino acids with incomplete sidechains and, except Ala, with a beta carbon)
  • ~incomplete_stdnucbase_c5primes (only the C5' atoms of standard nucleotides with nitrogen atoms but incomplete bases; nitrogen is always the first atom bonded to the ribose or deoxyribose)
  • Examples are below.
  • There are also additional more specific terms.
• X marks non-standard residues (other than D-amino acids). Find: ~nonstandard_residues and not ~d_aas or ~nsr and not ~d_aas.
• D marks D-amino acids. Find: ~d_aas
• ? marks anomalous atoms. Find: ~anomalous_atoms

• 6hww has 588 incomplete sidechains, which are 89% of its 663 amino acids.
• Unsimplified 5x50 has 790 incomplete sidechains, which are 21% of its 3,829 amino acids.
• 5x9z has 3,099 incomplete sidechains for 91% of its 3,418 amino acids.
• 2ace, in contrast, has 46 incomplete sidechains, 4% of its 1,054 amino acids.

• In the Find.. dialog (Focus Box) after specified atoms have been identified with yellow halos. Halos can be applied to a chain, ligand, etc. by clicking its name in the Molecule Information tab.
• In the Ends.. dialog (Molecule Information tab/Tools tab) after one end of a chain has been displayed.
• For Protein Crosslinks (Tools tab), after one crosslink has been displayed.

• Extensive introductions and explanations are linked.
• Although designed for examining details of a few residues, the map viewer is capable of showing the map for thousands of atoms. Examples with different resolutions, listed below, could be used for teaching purposes.
• FirstGlance determines whether the map is available before attempting to display it. The PDB began requiring deposition of maps with models in 2008. Entries deposited earlier often lack map data.
• The map isomesh can be shown within 3, 5, or 15 Å of the target atoms.
• The atomic model within the isomesh can be hidden.
• For X-ray models, the electron density map can be displayed for all features (2Fo-Fc), or for differences between the map and the atomic model (Fo-Fc).
• The target atoms are shown as sticks within the map. A checkbox displays them as balls and sticks.
• Slab thickness can be varied, or slab can be turned off (thickness 100%).
• The target atoms are colored by chemical element, with options to color them by absolute or relative temperature/B factor.
• Static images or presentation-ready animations (example at right) can be saved. See examples of static images for all-features and difference maps at Electron Density Maps in Proteopedia. More animations are in the slides that illustrate various animations saved from FirstGlance: tinyurl.com/movingmolecules.
• Density map methods used by FirstGlance/JSmol are described.

Biological Unit 1 of the Simian Virus 40 capsid (slabbed half) constructed from the crystallographic asymmetric unit and simplified to every 5th alpha carbon by FirstGlance in JSmol.

• Crystallography:
  Fewer chains than asymmetric unit:
  • 1KPL AU: 4 chains (1 sequence), 1 BU: 2 chains.
  • 4b14 AU: 3 chains, 3 BU 1 chain each. Only chain C has missing residues, including one within-chain gap.
  • 2vxj AU: 24 chains, 24 BU all monomers. Polypeptide chains are A-X. Glycosylating polysaccharides are the assigned chain IDs Y, Z, and a-v; these are excluded when counting chains per BU.
  • 2zzs AU: 32 chains, 32 BU all monomers. Tied with 4dx9 for most biological units per entry in the wwPDB. See Believe It Or Not!
  • 6nca AU: 60 chains, 3 sequences, 20 BU all trimers.
    
    Same, Fewer or More chains than the asymmetric unit:
  • 3m6y AU: 4 chains (1 sequence), 4 BU: 4, 4, 2, 2.
  • 1nek AU: 4 chains, 4 sequences, 3 BU: 4, 12, 8 chains.
  • 1zw0 AU: 8 chains (1 sequence), 15 BU: 2,2,2,2, 16,16, 8,8,8, 6,6,6,6, 4,4 chains. Has missing residues.
    
    More chains than the asymmetric unit:
  • 2ds7 AU: 1 chain, 1 BU: 2 chains. Has missing residues.
  • 1buu AU: 1 chain, 2 BU: 3, 3 chains, completely different from each other!
  • 7mgp AU: 1 chain, 1 BU: 6 chains. Has missing residues including a within-chain gap.
  • 1hho AU: 2 chains, 2 sequences, 1 BU: 4 chains.
  • 1sva AU: 6 chains, 1 sequence, 1 BU: 360 chains (virus capsid). Has missing residues.
  • 1ej6 AU: 5 chains, 3 sequences, 1 BU: 300 chains (reovirus core).
  
  
• Electron Microscopy:
  • 6nef: 1 chain, 1 BU: 9 chains (filament).
  • 4uft: 2 chains, 2 sequences (1 protein, 1 RNA), 1 BU: 78 chains (helical measles virus nucleocapsid with RNA).
  • 6f2s: 22 chains, 5 sequences (3 protein, 2 DNA), 1 BU: 220 chains (unusual "double" virus capsid).
• Special Cases
  • 2hhd AU: 4 chains, 1 BU: 4 chains. REMARK 350 specifies "Biomolecule 1" identical to the deposited asymmetric unit.
  • 4a53 NMR. REMARK 350 (which specifies biological units) is absent (as of March, 2022; wwPDB is gradually adding REMARK 350 to such entries). Absence of REMARK 350 was typical of about half of the NMR results in the wwPDB, mostly those deposited before 2011.
  • 5vln NMR. REMARK 350 is present, but specifies "Biomolecule 1" identical to the deposited model. This was typical of about half of the NMR results in the wwPDB, including recent depositions. The wwPDB is gradually adding REMARK 350 to such entries.
  • 4by9 AU: 18 chains, 5 sequences, 1 BU: 18 chains. Has a single "AND CHAINS:" line in REMARK 350.
  • 6rd4 AU: 31 chains, 18 sequences, 1 BU: 64 chains. Multiple "AND CHAINS:" lines in REMARK 350.
  • 7o3e has 31 chains with 23 distinct sequences. Some chain IDs are lower case. BU1 = the AU.
• Query Parameter "bu="
  • 1zw0: &bu=5 (Biological Unit 5) Testing BU number other than the default = 1.
  • 1hho: &bu=2 (Biological Unit 2) Testing handling of non-existent BU number.

1. Each asymmetric unit chain and its duplicates get a single distinct color*.
2. Each group of sequence-identical chains gets a distinct color*.
3. Distance from the center of the structure in spectral colors.
4. Distance from the center of the structure in grayscale. This emphasizes the depths of valleys in a surface.
   * Colors duplicate when more than 26 are needed.

Reovirus Core 1ej6. 300 chains: 60 duplicates of the 5 chains in the asymmetric unit.
1. Five Duplicated Chains	2. Three Distinct Sequences	3. Color by Distance	4. Grayscale by Distance

Example: 3iyv, a 21 MDa clathrin cage 740 Å in diameter. The Molecule Information Tab reports that it has been simplified to every 8th alpha carbon. A more detailed view (every 2nd alpha carbon) is offered (see Option below), but provides few if any additional insights (see snapshots at right, colored by distance from center). See also an animation. In the Views tab, click Solid to see the Å values of the exaggerated radii of the alpha carbons, as well as other color schemes.

Example: Biological Unit 1 of 5x9z is a single protein chain of 2,217 amino acids (no ligands+). Although all of these residues were present in the crystallized protein, the low resolution (7 Å) X-ray model is missing 507 (23%). In addition, 1,551 amino acids (91% of those present) are modeled missing one or more sidechain atoms. Thus, while the crystallized protein was 253 kDa, the atoms present in the model total only 112 kDa. The full protein mass (including ligands+, excluding water) is available from RCSB. When Biological Unit 1 differs from the deposited model, the correction must be applied (1/2 in the case of 5x9z). When not simplified, FirstGlance reports the mass of the atoms actually present in the model of Biological Unit 1 in its Molecule Information Tab (excluding missing residues, incomplete sidechains, and usually excluding hydrogen).

• Omit Hydrogen: When the model to be shown has > non-hydrogen atoms (9% of 187K entries in the wwPDB, ~18K entries*), hydrogen atoms (if present) will not be loaded. This will speed up loading and improve smoothness and efficiency of all FirstGlance operations. Hydrogens are present in only 16%* of the models in the wwPDB. The detection of non-covalent bonds by FirstGlance does not depend on hydrogens.
  Examples:
  • 6quk (glucose isomerase, X-ray, 1.6 Å) biological unit 1: 176 kDa, 14,114 non-H atoms (all protein and ligands+), 11,788 H atoms, total 25,902 atoms, 2 copies of the asymmetric unit.
  • 4xbf (histone demethylase complex with RNA, an epigenetic regulator, X-ray, 2.8 Å) biological unit 1: 370 kDa, 25,944 non-H atoms (25K protein + 0.3K RNA), 25,700 H atoms, total 51,644 atoms, 4 copies of the asymmetric unit.
  
  
• Only Backbone Atoms Option: When the model to be shown has to 99,999 non-hydrogen atoms (3% of 187K entries in the wwPDB, ~6K entries*), the user will be offered the option to display a simplified model containing only backbone atoms:
  • the alpha carbon atoms of protein, plus
  • the backbone phosphorus atoms of nucleic acids, plus
  • ligands+.
  In FirstGlance, Backbone atoms are distinguished from main chain atoms.
  ➤In proteins, "main chain atoms" include all non-sidechain atoms in amino acids. The non-H main chain atoms of each amino acid are N-Cα-C=O, that is, the N-Cα-C that form the polypeptide chain, plus the double bonded-oxygen on the carboxy C that gives partial-double-bonded character to each peptide bond. For a clear 3D illustration, see the 1 minute 15 second portion starting at 35 seconds and ending at 1:50 in this youtube video.
  ➤In polynucleotides, "main chain atoms" of each nucleotide are the phosphate plus ribose or deoxyribose, that is, the phosphoriboses or phosphodeoxyriboses. The bases are not part of the main chain. See the interactive DNA Structure tutorial at MolviZ.Org.
  Examples:
  • 4aoj (tyrosine kinase, X-ray, 2.8 Å) biological unit 1: 448 kDa, 25,648 non-H atoms (protein with ligands+), 0 H atoms, 4 copies of the asymmetric unit. Has missing residues.
  • 6cri (HIV Nef resistance to immunity, EM, 7 Å) biological unit 1: 886 kDa, 50,445 non-H atoms (protein with GTP ligands), 0 H atoms, identical to the asymmetric unit.
  • 1hqk (icosahedral hollow cage of lumazine, X-ray, 1.6 Å) biological unit 1: 1.0 MDa, 80,220 non-H atoms (all protein), 0 H atoms, 160 Å in diameter. Wall thickness ~35 Å. 12 copies of the asymmetric unit.
  • 6hkt (six nucleosomes, X-ray, 9.7 Å) biological unit 1: 1.4 MDa, 82,122 non-H atoms (protein and DNA), 0 H atoms, identical to the asymmetric unit.
  • 4ioa (50S ribosomal subunit, X-ray, 3.2 Å) biological unit 1: 1.4 MDa, 83,879 non-H atoms (protein and RNA), 0 H atoms, identical to the asymmetric unit.
  
  
• Only Backbone Atoms: When the model to be shown has ≥ non-hydrogen atoms (1.3% of 187K entries in the wwPDB, ~2.5K entries*), a simplified model (as above) will be displayed unconditionally. (You can prevent simplification with the query parameter &nosimp.)
  Examples:
  • 1a34 (icosahedral satellite tobacco mosaic virus capsid with RNA, X-ray, 1.8 Å) biological unit 1: 1.5 MDa, 105,780 non-H atoms (69K protein, 26K RNA), 103K H atoms, 60 copies of the asymmetric unit, 10,020 residues modeled. 170 Å in diameter.
  • 7o3x (thylakoid membrane remodeling structure, EM, 3.9 Å) biological unit 1: 2.6 MDa, 148,395 non-H atoms (protein and ADP), 0 H atoms, 15 copies of the asymmetric unit, 19,305 residues modeled. ~300 Å in diameter.
  
  
  
• Subset of Backbone Atoms: When the simplified model has > alpha carbon or phosphorus atoms (0.7% of 187K entries in the wwPDB, ~1.3K entries*), it will be further reduced to <  atoms by loading only a subset of the alpha carbons/nucleic acid phosphorus atoms along with all ligands+.
  Examples:
  • 2gtl (annelid respiratory poly-hemoglobin, X-ray, 3.5 Å) biological unit 1: 3.4 MDa, 235,776 non-H atoms (protein with hemes), 0 H atoms, 12 copies of the asymmetric unit. 14,376 alpha carbons are loaded (1/2 of the total of 28,788). Has missing residues. Took 105 seconds to load without simplification (query parameter &nosimp) vs. 12 seconds with default simplification.
  • 1aym (human rhinovirus 16 capsid, X-ray, 2.2 Å) biological unit 1: 5.7 MDa, 418,500 non-H atoms (all protein), 0 H atoms, 60 copies of the asymmetric unit. 310 Å in diameter. 24,120 alpha carbons are loaded (1/2 of the total of 48,240).
  • 3iyv (clathrin coat, EM, 8 Å) biological unit 1: 21 MDa, 183,600 alpha carbon atoms only, 0 H atoms, 12 copies of the asymmetric unit. 740 Å longest outside dimension. 22,956 alpha carbons are loaded (1/8 of the total of 183,600).
  • 1ej6 (reovirus mRNA-synthesizing & exporting core, X-ray, 3.6 Å) biological unit 1: 31 MDa, 2,069,220 non-H atoms (all protein), 0 H atoms, 60 copies of the asymmetric unit. 720 Å in diameter. Wall thickness ~50-100 Å. 23,880 alpha carbons are loaded (1/11 of the total of 262,200).
  • 6q5u: 2.28 million atoms.
  • 7vrn: 2.48 million atoms.
  • 1wce (double-stranded RNA avian birnavirus capsid, X-ray, 7 Å) biological unit 1: 37 MDa, ~2,600,000 non-H atoms (all protein), 0 H atoms, 60 copies of the asymmetric unit. 700 Å in diameter. 23,760 alpha carbons are loaded (1/14 of the total of 331,980). Asymmetric unit has only alpha carbons.
  • 8w9p: 4.58 million atoms.
  • 5zvt (double-stranded RNA aquareovirus capsid, EM, 3.3 Å) biological unit 1: 37 MDa, ~5,258,700 non-H atoms (all protein, 6 sequences), 0 H atoms, 60 copies of the asymmetric unit. ~750 Å in diameter. 24,840 alpha carbons are loaded (1/28 of the total of 695,520). Asymmetric unit has 87,645 non-hydrogen atoms.
  • 1m4x (Paramecium Chlorella DNA virus capsid, EM, 28 Å) biological unit 1: ~231 MDa, ~16,284,240 non-H atoms (all protein), 0 H atoms, 1,680 copies of the asymmetric unit. 1,800 Å in diameter. 25,200 alpha carbons are loaded (1/84 of the total of 2,081,520). The model has 5,040 chains, each with 413 residues. The default view showing 1/84 alpha carbons represents each chain by only 4-5 atoms. Optionally, you can load 1/21 alpha carbons, representing each chain by 19-20 atoms.
  
  
• More Backbone Atoms:
  • Option 1: When a subset of < backbone atoms is displayed by default, you will have the option of displaying a larger number of backbone atoms, not to exceed . This will be at the expense of more sluggish performance (be patient). Snapshots of a clathrin cage (3iyv) are shown above, represented by the default of 23K backbone atoms (every 8th), or the option of 92K backbone atoms (every 2nd).
    Examples:
    • 1aym rhinovirus capsid: Instead of every 2nd alpha carbon (24,120, see above) you can display all 48,240 alpha carbons.
    • 3iyv clathrin cage: Instead of every 8th alpha carbon (22,956, see above) you can display every 2nd alpha carbon (91,824). Compare snapshots above.
      
  • Option 2: If you want to try an arbitrary subset of the backbone atoms, use the query parameter &bbonly=N. For example, to load every 3rd backbone atom, use &bbonly=3. To load all backbone atoms, use &bbonly=1.
  
  Test Set: Here is a small set of PDB IDs for testing a range of biological unit and simplification levels. For more details about each case, see above. Note that you can also test simplification levels on any model using query parameters.
  † Tests with lower case chain names/IDs.
  ‡ Tests with symmetry-generated multiple-character chain names/IDs.
  • 1i8L: X-ray, 4 chains in the asymmetric unit, 2 chains in each of 2 biological units. No duplication, no simplification. Missing residues, incomplete sidechains, ligands. No water.
  • ‡ 7mgp: X-ray, one chain duplicated to make 6, no simplification (all atoms loaded), missing residues, incomplete sidechains, alternate locations. Has water.
  • † 3Lo3: Asymmetric unit has 28 chains A-Z + lower case a, b, all of a single sequence. Biological units are 14 dimers. Biological Unit 13 is a + b. Water count varies per dimer.
  • ‡ 6nef: EM, one chain duplicated multiple times, optional backbone atoms only, all alpha carbons loaded, no missing residues.
  • ‡ 4aoj: X-ray, 3 sequence-identical chains duplicated multiple times, optional backbone atoms only, all alpha carbons loaded, missing residues indicated with empty baskets. When simplified, not mentioned are incomplete sidechains and alternate locations. Has both alpha helices and beta strands, and water.
  • ‡ 2gtl: X-ray, 15 chains duplicated multiple times, unconditionally backbone atoms only, every 2nd alpha carbon loaded. Missing residues NOT indicated with empty baskets. Some 3-character chain IDs.

• ConSurf result with less than non-H atoms: All non-H atoms will be loaded. Example:
  • Enzyme 1e8f (34,568 non-H atoms, 4,360 modeled alpha carbons).
  
  
• ConSurf result with between and non-H atoms: the user is offered the option to simplify to backbone atoms (alpha carbons and nucleic phosphorus atoms) plus ligands. In this size range, the number of backbone atoms will be ~20,000, which gives smooth performance. Example:
  • Oblate phage Qβ particle 7LGG (148,950 non-H atoms, 19,800 modeled alpha carbons).
  
  
• ConSurf result where non-H atoms exceed , and backbone atoms do not exceed : automatic simplification to backbone atoms + ligands. Examples:
  • Eukaryotic vault 6bp8 (480,246 non-H atoms, 60,996 alpha carbons).
  • Bacteriophage HK97 capsid 1ohg (904,200 non-H atoms, 117,600 modeled alpha carbons).
  
  
• ConSurf result where the number of backbone atoms is between and : asymmetric unit is recommended but option to load all backbone atoms if the user is willing to wait several minutes and accept very sluggish performance. Example:
  • Eastern Equine Encephalitis Virus capsid + heparin, 6odf (1,588,920 non-H atoms, 203,760 alpha carbons).
  
  
• ConSurf result where the number of backbone atoms exceeds : Biological Unit is too large for FirstGlance; asymmetric unit will be offered. If the user wishes to be extremely patient to color the biological unit, the query parameter &bbonly=1 can be used. Example:
  • Human papilloma virus 16 capsid + Fab antibody, 6bt3 (3 protein sequences, 2,122,980 non-H atoms, 274,320 modeled alpha carbons).

In this group, Biological Unit 1 is identical with the deposited model, and no secondary structure is specified:
• 1qo1 protein only (ATP synthase motor, X-ray, 3.9 Å)
• 1qzb RNA only (tRNA, EM, 9 Å)
• 1bdx protein and DNA (helicase RUVA with Holliday junction, X-ray, 6 Å)
• 6zig protein only (bacteriophage baseplate, EM, 42 Å)
• 2rcj protein only (IgM pentamer, solution scattering)
  
  
• Simplified Biological Unit 1 of 3iyv has 12 copies of the deposited model, and no secondary structure is specified.
• Asymmetric unit of 3iyv, protein only (clathrin coat, EM 7.9 Å).
  
  These are unusual because they specify secondary structure (HELIX and SHEET records in PDB format):
• 1a1d protein only by NMR (RNA polymerase subunit). No biological units specified.
• Asymmetric unit of 3j3p, protein only (Fab-coated polio virus capsid, EM, 9 Å). Simplified Biological Unit 1 of 3j3p has 300 chains, 60 copies of the 5-chain asymmetric unit. Shown at right.
  
  Mixtures of all non-H atoms and only backbone atoms:
• 1mj1, Protein and RNA (3 ribosomal proteins, elongation factor TU, tRNA, and fragments of 23S ribosomal RNA). Protein chains L, O, P have alpha carbons only. Protein chain A has main chain atoms only (no sidechain atoms). tRNA chains C, D have all non-H atoms. RNA chains Q, R have phosphorus atoms only. Secondary structure records for chain A only.
• 1LBG, Protein and DNA (lac repressor bound to DNA). Protein has alpha carbons only. DNA has all non-hydrogen atoms. Has HELIX/SHEET records.
• Unsimplified 4ioa, Protein and RNA (large ribosomal subunit, X-ray 3.2 Å). 2 RNA chains and 25 protein chains modeled with all non-H atoms, plus 3 protein chains named "1", "2", and "3" with only alpha carbons. Has HELIX/SHEET records.
• 486d, RNA (ribosomal RNA, X-ray, 7.5 Å). Has 5 RNA chains with all non-H atoms, plus 2 RNA chains (F and G) with only backbone phosphorus atoms.

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

• Subset 1 is selected with not (protein or nucleic or water).
  
  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 octane in 1APM.
  
  
• Subset 2 includes standard amino acids or nucleotides that are not part of a polymer chain (isolated single residues, single residue "chains") or that lack certain standard atoms. If not included in Ligands+, these would be invisible in displays such as Cartoon, Secondary Structure, N->C Rainbow, and Vines with sidechains hidden. Examples include GLY308 in 4CPA, and A351 in 1BKX. Further examples are listed in the lower left help panel displayed when you depress the Ligands+ button in the button box. You can use the Find.. dialog in the Focus Box with these terms:
  • Monomeric amino acids: ~unchained_aas (Technical: limited to residues/groups deemed "protein" by Jmol, with polymerlength=0.)
  • Monomeric nucleotides: ~unchained_nucleotides, ~unchained_nucleosides (Technical: limited to residues/groups deemed "nucleic" by Jmol, with polymerlength=0.)
  
  
• Subset 3 is dipeptides which are deemed ligands by the policy of the World Wide Protein Data Bank. For more information, see above. Dipeptides can be found with the term ~dipeptides (using the Find.. dialog in the Focus Box).
  
  See also anomalous atoms.

• Non-standard amino acids:
  • 1k28 (selenomethionine)
  • 1bkx (phosphoserine, phosphothreonine)
  • 8g82 (many non-standard amino acids)
• D-amino acids: 5e5t (and see below)
• Non-standard nucleotides: 1evv

• The 20 historically standard L-amino acids, plus ambiguous residue codes ASX, GLX, and unknown UNK (see UNK below).
• Actually, there are now 22 amino acids deemed "standard" for 3D structure models. In 2014, the Protein Data Bank included two additional genetically encoded proteogenic L-amino acids as "standard", namely pyrrolysine (PYL, O) and selenocysteine (SEC, U). In other contexts, those two additional amino acids may still be termed "non-standard".
• Eleven standard nucleotides A, C, G, I, U, DA, DC, DG, DI, DT, and DU plus unknown nucleic residues N (see N below).
  • 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.
  • "T" (ribothymidine, as distinct from DT) is not listed in the PDB format, but "T" is recognized by Jmol. Ribothymidine is designated 5MU (5-methyluridine 5'-monophosphate) in wwPDB entries, for example 1i9v. Find T and RNA.
  • GMP, GDP, and GTP (and the same for the other bases) are also deemed standard nucleotides because when you select G, Jmol also selects those. Example: GTP in 1qln.

• D-amino acids are labeled "D", instead of the "X" used for other non-standard residues. To hide the D labels, see Labels.
• The count of D-amino acids, and their percentage of non-Gly amino acids are reported in the Molecule Information Tab. The count of D-amino acids is also alerted at the outset as unusual components.
• Incomplete sidechains in D-amino acids are now marked S— and reported in the Molecule Information Tab. ("S—" supercedes "D"). Example: 5e5t. (Click on "incomplete sidechains" in the Molecule Information Tab to put halos on S— residues.)
• Hydrophobic/Polar (Views tab) colors D-amino acids correctly.
• Charge (Views tab) now colors and counts D-amino acid charges correctly. Examples are given in the lower left (help) panel.
• Disulfides/S/Se (Tools tab) now handles Dcy-Dcy and Cys-Dcy disulfide bonds correctly. Examples are given in the lower left (help) panel.
• Salt Bridges/Cation Pi (Tools tab) now reports salt bridges and cation-pi interactions involving charged sidechains of D-amino acids. Examples are given in the lower left (help) panel.
• Protein crosslinks are detected for both D and L amino acids.

• This method works correctly only when all atoms (notably including the standard main-chain atoms) in non-standard residues are deemed HETATM in the PDB file. Examples include the many non-standard nucleotides in the t-RNA 1EVV (2MG, H2U, M2G, OMC, OMG, YG, PSU, 5MC, 5MU, 7MG, and 1MA), the non-standard seleno-methionines in 1H3O, and the non-standard phosphorylated serines and threonines in 1BKX. Typically, in these cases, the entire non-standard HETATM residue is given a non-standard PDB residue code name, such as MSE for selenomethionine, SEP for phosphoserine, or TPO for phosphothreonine. The corresponding full names can be seen in the MODRES or HETNAM records in the PDB file header (available from pdb.org, e.g. Header of 1EVV), or by clicking the PDB or OCA links in control panel (upper left) of FirstGlance.
  
  
• This method fails when an alternative convention is used in the PDB file: designating the standard main-chain atoms within a non-standard residue as ATOM, and only the non-standard atoms as HETATM. An example is GLY5 with PYL1005 in 1B07. In such cases, FirstGlance displays the non-standard portions of these residues as "Ligands+". (Many earlier such cases were fixed in remediations. For example, SER or THR plus PHO became SEP or TPO in remediated 1apm.)
  
  
• This method fails when Jmol fails to recognize the residue as protein or nucleic. For example, OPR in chain F of 1ucy has a standard arginine sidechain, but it has two extra carbons in the main chain, causing Jmol not to recognize it as "protein". Thus, it is not labeled X, but because all of its atoms are HETATM, it is treated as Ligands+.
  
  

1QLN
Unsimplified 4ioa
Unsimplified 1fka

• Alpha carbons only: If all or some amino acids are modeled as alpha carbons only, that is reported. Examples:
  • Some alpha carbons only: Unsimplified 4ioa.
  • All alpha carbons only: 1jgo.
  
  
• Reported only when showing more details:
  
  
  • Main chain atoms only: If some non-glycine amino acids are modeled with only main chain atoms, that is also reported. Example:
    • 1QLN.
    • 1mj1.
      • 366 (51%) non-glycine main-chain only amino acids.
      • 382 (48.5%) alpha-carbon-only amino acids, including 33 glycines.
      • 39 glycines that have all non-hydrogen main-chain atoms.
      • 787 TOTAL alpha carbons.
      • No beta carbons, so no sidechains.
    
    
  • Incomplete sidechains are common. Examples:
    • 4bxf.
    • Unsimplified 1fka:
      • 1,561 amino acids (84% of all 1,864 amino acids) have incomplete or missing sidechains. These include:
        • 5 UNK modeled as main chain atoms only.
        • 795 UNK modeled as alpha carbons only.
        • 761 standard amino acids with incomplete sidechains (none Ala, so all have beta carbons).
      • The total of 1,864 alpha carbons is made up of:
        • 1,561 with incomplete or missing sidechains.
        • 129 standard amino acids with complete sidechains.
        • 174 UNK with beta carbons (so modeled as Ala), thus not designated as "missing sidechains".
      • 974 amino acids (52%) are unknown (UNK), which include all 795 modeled as alpha carbons only, plus 174 UNK modeled as alanines§, plus 5 UNK modeled as main chain atoms only (so modeled as glycines).
        • § Using the Find links to reveal terms beginning with tilde, you can construct, for example, a Find.. query for the 174 alpha carbons of UNK amino acids modeled as alanines: ~alphacarbons and unk and not ~alphacarbonsonly and not ~mainchainonly_alphacarbons
        • ~alphacarbons is mentioned in the help below the Find.. slot.
      • 21% of RNA nucleotides are modeled as phosphoribose only.
    
    
  • D-amino acids: Example: 2soc. For more examples, see D-Amino Acids.
    
  • Amino acids lacking main-chain N or C. Example: 4en3. More examples at Unusual Components or Features.
    
  • Amino acids lacking main-chain O. Example: 1uc5. More examples at Unusual Components or Features.
    
  • Amino acids with no alpha carbon. Examples: 1h3o, 1usi. More examples at Unusual Components or Features.
    
  • Unknown amino acids UNK or UNX. Example: 3hm6. More examples at Unusual Components or Features.

Counting Nucleotides: P vs. C5'

1jgo
6e1w
Asymmetric Unit of 1a34

C5' Count: In most cases, the number of nucleic C5' atoms (which occur in both ribose and deoxyribose) is the best estimate of the number of nucleotides. Therefore, FirstGlance reports the nucleic C5' count by default (in the

• DNA: 1ijw, 1flo.
• RNA: 1u6b, 1ehz.
• Both: 104d, 1hmh.
  
  *Distinguishing polynucleotides from monomeric nucleotides is challenging, due to the occasional nucleotide modeled as a phosphorus atom alone, or PO₃ alone, or phosphoribose without a base, or an unknown nucleic residue [N]. However, in most cases, monomeric nucleotide or nucleoside ligands are identified correctly. See monomeric nucleotide ligands.
  
  Examples with Unknown Nucleic Residues "N":
  Note that alternate locations are shown when FirstGlance is showing "more details", but hidden when showing "fewer details". When showing "more details", to limit Find.. to the first conformation, add to the query "and conformation1" (no space before 1).
  
  
  • An example with both 37 UNK (unknown amino acids) and 53 N is 6n7r. The N residues are modeled as A:U pairs in a double helix. The UNK residues are modeled as Ala.
  • 6d06 has 1 unknown RNA nucleotide N11 in chain C. It is modeled as phosphoribose with no base. (No alternate locations here.)
  • The asymmetric unit of 7Lph has 1 unknown RNA nucleotide N1 in chain A (with 2 alternate locations). It is modeled as phosphoribose with no base.
  • The 2i82 has 1 RNA nucleotide designated N1208 in chain E. It is modeled with ribose and a non-standard fluoro-pyrimidine base. There are 21 nucleotides with 21 C5' atoms, but only 20 P atoms because the 5' terminal nucleotide G1201 is not 5'-phosphorylated. (No nucleotide atoms have alternate locations.)
  • The asymmetric unit of 3dzi is modeled with one N301 ligand modeled as phosphoribose (no base). There are no polynucleotides. There are 3 nucleotide P atoms, and 3 C5' atoms. (No alternate locations here.) Other cases with N ligands: 1g9s, 1phw, 8u0z.
  • 6kr6 has 1 unknown nucleic residue N5 in chain B modeled as PO₃ (no ribose, no base). Since the 5' terminus of chain B is phosphorylated, there are 5 nucleic P atoms. But since C5 lacks a ribose, there are only 4 nucleic C5' atoms. (No nucleotide atoms have alternate locations.)
  • 7e9e has 2 unknown RNA nucleotides N13-14 in chain A modeled as phosphoriboses (without bases). N13 has 2 alternate locations. In conformation 1 there are 32 nucleic *.P and 33 *.C5'. The 5' terminal nucleotide C1 is not 5'-phosphorylated.
  • 6e1w has 2 unknown RNA nucleotides, N13-14. N13 is modeled as PO₃ alone, while N14 is modeled as phosphoribose. There are 32 nucleic P atoms and 32 C5' atoms. The numbers are equal because while N13 lacks C5', the 5' terminal nucleotide C1 is not 5'-phosphorylated. (No alternate locations here.)
  • 7oqe has 53 unknown nucleic residues [N] in chain I represented by RNA phosphoriboses (without bases). There are 787 C5' atoms, but only 786 nucleic P atoms. 50 P atoms have 4 oxygens each; The two 5' terminal P atoms have only 3 oxygens each.
  • 1dv4 has all 361 nucleotides modeled as phosphoriboses, and all are unknown "N". There are only 342 P atoms because the RNA chain A has many breaks, with the 5' ends unphosphorylated. 314 P atoms are modeled with 2 oxygens each; 28 are modeled with 1 oxygen each.

• 1mj1: mixture of 152 nucleotides modeled with all non-H atoms and 68 modeled as P atoms only.

• Unsimplified 1fka: 21% of RNA nucleotides are modeled as phosphoribose only.
• 6d06 has 1 unknown RNA nucleotide N11 in chain C. It is modeled as phosphoribose with no base.
• 6e1w has 2 unknown RNA nucleotides, N13-14. N13 is modeled as PO₃ alone, while N14 is modeled as phosphoribose.
• 1fyk has 8 unknown DNA nucleotides modeled as 6 phosphodeoxyriboses, with the 5' ends of the 2 tetramer chains unphosphorylated (so the N1 residues are just deoxyriboses).
• 7oqe has 53 unknown nucleic residues [N] in chain I represented by RNA phosphoriboses (without bases).
• 1dv4 has all 361 nucleotides modeled as phosphoriboses, and all are unknown "N".

• 6kr6 has 1 unknown nucleic residue N5 in chain B modeled as PO₃ (no ribose, no base).
• 6e1w has 2 unknown RNA nucleotides, N13-14. N13 is modeled as PO₃ alone, while N14 is modeled as phosphoribose.
• The asymmetric unit of 1s47 has 4 DNA nucleotides modeled as phosphates only.

• 1mj1: mixture of 152 nucleotides modeled with all non-H atoms and 68 modeled as P atoms only.
• 1jgo: mixture of 232 nucleotides modeled with all non-H atoms and 1,540 modeled as P atoms only.

(DNA in 1d66, 1ijw, 1flo;
RNA in 104d, 1u6b),

(DNA in 1l1m, 1QLN;
RNA in 1evv, 1ehz; 1hmh has 2 chains, one P-lated, the other not).

(DNA in 1flo;
RNA in 1u6b).

Amino acids are labeled S— (incomplete sidechains) when they are one of the 22 standard amino acids modeled without one or more non-hydrogen atoms. They are labeled S— (see Labels), and when FirstGlance is showing more details, reported in the Molecule Information Tab. To locate these amino acids, click the Find links next to the reports of the numbers of incomplete sidechains, main-chain only amino acids, or alpha-carbon only amino acids (see snapshots of examples). For more flexiblity, using Find.. (in the Focus Box), enter the terms listed under Labels (or, in more detail, under Finding Backbone Atoms) to put yellow halos on alpha carbons or all atoms of residues with missing sidechain atoms.

• 1BL8
• 1APM.
• More examples under Counting Amino Acids.

• 1q29 is missing a single atom, N2, from G18:A, marked S—.
• 1i9v has 1 entire base missing at U39. Its phosphate and ribose are made obvious as Ligands+, and it is announced in the Molecule Information Tab.
• The asymmetric unit of 1s47 has 4 nucleotides with their entire deoxyriboses and bases missing. Only the phosphate is present, which is made obvious as Ligands+, and these are announced in the Molecule Information Tab.

• Unsimplified 1fka

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. u50 and sidechain (sidechain only of uridine 50, e.g. in 7UCR)
8. gly.ca (carbon-alpha in glycine), or gly and ~alphacarbons.
9. ~alphacarbons (or ~calpha) for all alpha carbons. CAUTION: *.ca includes calcium or alpha carbons, e.g 2bbn.
10. carbohydrate for most sugars.
11. ~ligandsplus for all Ligands+.
12. ~nonstandard_residues or ~nsr for non-standard amino acids or nucleotides: those labeled X.
13. ~metals (Na+, K+, Mg++, Ca++, Zn++, etc. Complete list.)
14. met.sd (sulfur-delta in methionine)
15. mse (the group name for selenomethionine, e.g. in 1K28)
16. sulfur (all sulfur atoms; use full names for elements)
17. 12-23 (all residues/groups with sequence numbers in this range)
18. 12-23:b (residues/groups in chain B with sequence numbers in this range)
19. 12-23 and protein (excludes non-protein, such as water or DNA)
20. 12-23 and nucleic (excludes non-nucleic, such as water or protein)
21. temperature >= 100 (B-factor/temperature value)

19. sequence=tlyr or sequence=tga using one-letter residue codes for amino acids or nucleotides. These example sequences work with 1ijw.
20. chains(A, F17) (an arbitrary list of individual chains) ¶
21. seqid(A, D44) (all sequence-idential chains) ¶

• 5e01: protein A=B, DNA C=D.
• ‡ 1fhy: 4 identical DNA chains A, A1, B, B1.
• ‡ (biological units 2, 3) 1nek: 4 chains, 1 sequence, in its asymmetric unit; 8 and 12 chains in its biological assemblies.
• 1f02: 2 chains, 2 sequences in its asymmetric unit; 3 chains its biological assembly 1.
• 1pma: Proteosome, 28 chains, 14 of each of 2 sequences. Numeric chain names/IDs 1, 2.
• † 7o3e: 31 chains including many with lower case letter names (all unique sequences). Has chains e, k but not E, K; has P, Q but not p, q.
• † 8qbm: 29 chains, all single letters, lower case names in sequence-identical families: 6 + 5 chains protein, 6 RNA, 6 DNA.
• † ‡ 7txj: 2 sequences of protein (chains A, a), 1 sequence of DNA (chains 1, 2);
• ‡ 1f8v: Virus capsid with 2 protein sequences (180 + 180 chains) plus 1 RNA sequence (60 chains) forming a dodecahedral cage.
• ‡ 1m06: 180 chains of protein F, G, J; 60 chains X of non-standard residues modeled as (resolution 3.5 Å) chains of dideoxyribose phosphate.
• ‡ 5j37: 60 chains of protein, 12 each of A-A11 (B,C,D,E). 60 chains of DNA, 12 each of F-F11 (G,H,I,J).
  
  For Chain Details
• 1ucy: In biological unit 1 (BU1), all 4 chains are sequence-distinct. BU1 is smaller than the asymmetric unit (AU). "Find chain" not "Find group". "Find sequence-identical" not offered.
• ‡ 7mgp: BU1 has 6 chains duplicated from the single chain in the AU. "Find group" not "Find chain". "Find sequence-identical" not offered.
• ‡ 8y3j: BU1 has 180 copies of each of two sequence-distinct chains. "Find group" (not "Find chain") or "Find sequence-identical".
• 7WV3, header section removed (ATOM and HETATM records only). Compare with intact published 7wv3.
• AlphaFold CoLab Model with No Header Section.
• AlphaFold CoLab Model, No Header, pre-processed by ConSurf.

Salt Bridges/Cation-Pi
• CAUTION: Identification of Cation-Pi Interactions is approximate.
• ~all_sb, ~all_catpi (All cases in the model. Examples of use are in the report generated by List All after you click Salt Bridges/Cation-Pi (Tools tab).
• ~tac_sb, ~tac_catpi ("tac" = "Targets and Contacts". Cases in the most recent results from using Contacts & Non-Covalent Interactions in the Tools tab).
  
  Targets vs. Contacts in results from Contacts & Non-Covalent Interactions (Definitions)
• ~targ_hbonds, ~cont_hbonds (putative hydrogen bonds)
• ~targ_hphob, ~cont_hphob (apolar interactions)
• ~targ_sb, ~cont_sb (salt bridges)
• ~salt_bridged_cations, ~salt_bridged_anions, ~salt_bridged_ions, ~salt_bridged_amino_acids
• ~salt_bridged_nterm, ~salt_bridged_oterm (N-terminal cations, C-terminal anions involved in salt bridges)
• ~targ_catpi, ~cont_catpi (cation-pi interactions)
• ~catpi_cations, ~catpi_rings, ~catpi_amino_acids (cation-pi interactions)
• ~catpi_nterm (N-terminal cations involved in cation-pi interactions)
• ~targ_memi, ~cont_memi (metal and miscellaneous interactions)
  
  Backbone Atoms
  See also Backbone atoms vs. main chain atoms and Label S— and Counting Amino Acids and Counting Nucleotides.
• ~alphacarbonsonly (amino acids modeled with only their alpha carbon atoms)
• ~mainchainonly_alphacarbons (alpha carbons of amino acids modeled with only their main chain atoms; to find all atoms in those amino acids: within(group, ~mainchainonly_alphacarbons))
• ~incomplete_stdaa_sidechain_alphacarbons (alpha carbons of standard amino acids with one or more non-hydrogen atoms missing in their sidechains and, except Ala, with a beta carbon)
  
  
• ~nucleic_c5prime (C5' atoms in nucleic acids)
• ~nucleic_p (phosphorus atoms in nucleic acids, see Counting Nucleotides)
• ~nucleic_p_only (phosphorus atoms in nucleotides modeled with only their phosphorus atoms)
• ~nucleicPRiboseOnly_c5primes (C5' atoms in nucleic acids modeled with only their phosphoribose or phosphodeoxyribose atoms, without bases)
• ~incomplete_stdnucbase_c5primes (only the C5' atoms of nucleotides with nitrogen atoms but incomplete bases; nitrogen is always the first base atom bonded to the ribose or deoxyribose)
  
  Incomplete Residues/Sidechains
  See also S— Labels and Incomplete Sidechains.
• ~incomplete_sidechains (only the alpha carbons or nucleotide C5' atoms in amino acids with incomplete or missing sidechains or nucleotides with incomplete or missing bases)
  Definition: ~incomplete_stdaa_sidechain_alphacarbons or ~mainchainonly_alphacarbons or ~alphacarbonsonly or ~incomplete_stdnucbase_c5primes or ~nucleicPRibose_c4primes or ~nucleic_P_only
• ~incomplete_sidechain_residues (all atoms in the residues containing atoms in ~incomplete_sidechains)
  
  Unusual components: The complete list of terms for unusual components will be found under Unusual components or features.
• ~d_aas (D-amino acids, so, for example in 5i1n after showing all salt bridges, ~d_aas and ~salt_bridged_ions)
• ~cyclic_nucleotides (or ~cyclic_nucs)
• ~unchained_nucleosides ("unchained" meaning not part of a polynucleotide)
• ~unchained_nucleotides ("unchained" meaning not part of a polynucleotide)
• ~unchained_aas ("unchained" meaning not part of a polypeptide)

• @{locsPerAtomBitset[N]} (locations of atoms with N locations/atom)
• @{atomNthLocs[N]} (Nth locations of atoms)
• @{altLocMultBitset} (locations of all atoms with multiple locations)
  
  
• ~bbforks1 (conformation 1 of backbone atoms with alternate locations, "backbone forks")
• ~bbforks2 (conformation 2 of backbone atoms with alternate locations, "backbone forks")
• ~bbforks (both conformations of backbone atoms with alternate locations, "backbone forks")

• From within the Molecule Information Tab:
  • Clicking on a chain name/ID (A, B, C, etc.) finds that chain.
  • The Chain Ends dialog will find ends of chains, and zoom in automatically for a detailed view.
  • The elements dialog will find a chemical element.
  • Under Ligands+ & Non-Standard Residues, clicking the 3-character code for a compound finds it.
    
    In more details mode:
  • The Protein crosslinks dialog will find specific putative crosslinks. Example: 2xi9.
  • When alternate locations are present, that dialog can find several subsets of alternate locations.
  • When the occupancies of some atoms are less than 100%, that dialog can find atoms with various occupancy ranges.
• From within the Tools Tab:
  • Salt Bridges can find salt-bridged cations or anions or amino acids.
  • Cation-Pi Interactions can find cations or N-termini or aromatic rings or amino acids engaged in putative cation-pi interactions.
  • Amino acids with designated Evolutionary conservation levels can be found when the PDB file is pre-processed by the ConSurf server.

Note that "atoms with halos" (from Find..) can be designated as a target for the Contacts.. tool (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.

Atoms with halos can also be hidden or isolated (see Hide.. and Isolate.. in the Focus Box).

The Electron Density Map can be displayed for any set of atoms with halos.

		Enolase (4enl; a glycolytic enzyme) evolutionary conservation from ConSurf. Catalytic pocket is highly conserved. More..

• It is easy to use and fully automated. Step by step instructions.
• It uses state-of-the-art methods, all published in peer-reviewed scientific journals.
• When the multiple sequence alignment has insufficient data to assign a conservation grade to a residue (wide confidence interval), it is colored  yellow .
• Pre-processing of PDB files by the ConSurf Server (but not PDB files from ConSurfDB*) is automatically detected by FirstGlance: The initial display is colored by conservation, with a color key and convenience tools. See conservation of the catalytic site of enolase in FirstGlance.
  
  * The ConSurf Server puts a custom header into PDB files that communicates conservation results to FirstGlance. Unfortunately, that header was removed from the PDB files in ConSurfDB (DataBase) in 2022. Therefore, FirstGlance cannot display conservation results using PDB files from ConSurfDB. You must submit your PDB ID (or upload your PDB file) to the ConSurf Server in order to visualize conservation in FirstGlance.
  
  The ConSurf Server (Yariv et al., Protein Science, 2023) was first available in Fall, 2002 (Glaser et al., Bioinformatics, 2003). Between 2003 and 2006, visualization was with the now-defunct Protein Explorer (Glaser et al., Bioinformatics, 2003, Landau et al., Nucleic Acids Research, 2005). FirstGlance has been offered by the ConSurf Server as an option for visualization since Fall, 2006 (Ashkenazy et al., Nucleic Acids Research, 2010).

Conservation of residues in the peptide-binding groove of major histocompatibility (MHC) protein. Gray: 8-residue peptide fragment of vesicular stomatitis virus nucleoprotein. Most groove-lining residues are variable, due to numerous alleles of MHC enabling the groove to bind a broad range of peptides. Highly conserved are the groove residues contacting the carboxy terminus of the peptide (e.g. Lys 146), and forming the pocket for the anchor residue and amino terminus of the peptide (Tyr 7, Tyr 159). (Yellow, Trp147, insufficient data.) From 2VAA.

• The protein is automatically colored by conservation in the initial view, with a color key adjacent, and several convenience tools plus a chart (examples) showing the distribution of conservation grades (a chart not provided by the ConSurf Server), and the APD of the MSA.
• Biological Assembly 1 is the initial view (with options to view the asymmetric unit or other biological assemblies).
• Checkboxes apply conservation colors to all chains that are sequence-identical with the chain processed by ConSurf. Demonstration.
• Conservation of residues contacting any specified ligand or moiety can be seen using Contacts & Non-Covalent Interactions (Tools tab). See animation at right. Contacting residues and their conservation grades can be listed spreadsheet-ready for analysis: Sample Listing with Procedure.
• Conservation of salt-bridged residues is easily seen by clicking Salt Bridges/Cation-Pi (Tools tab). All salt bridges with their conservation values can easily be listed, spreadsheet ready.

  Example: beta-galactosidase homotetramer. DECLINE the offer to simplify the model (else salt bridges will not be present). After "BUSY" disappears, click Go to the FirstGlance Control Panel. Click the Tools tab near the upper left. Click Salt Bridges/Cation-Pi. After the salt bridges appear, note that you can color them by conservation using a checkbox in the left middle, ConSurf Colors. Click the yellow List All button (see snapshot at left).

• Conservation of any specified residues is easily seen using Find.. (Focus box).
• Conservation of any of the previous three sets can be listed in spreadsheet-ready text for analysis by sorting, averaging, linear regression or correlation. Example: Contacts to chain A of 1vao from ConSurf pre-processed 1vao.
• Step by step guidance: Visualizing Conservation in FirstGlance, which also has more examples.

• Additional helpful guides: Index to ConSurf Articles in Proteopedia.

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 Find.. (in the Focus Box, which is in any tab except Resources or Preferences) to apply halos to atoms that you specify. Halos are bright yellow rings around atoms (see snapshots at right -- touch snapshots with your mouse for more information).
   
   
2. "Chain" vs. its associated Ligands+, non-standard residues, and water. You can click on a chain of amino acids or nucleotides to select it as a target to visualize the atoms that contact that target. Ligands+ and water associated with a chain, and non-standard residues that are part of a chain sequence, are typically assigned the same chain ID as the chain. For example, in the DNA chain B of 1ijw, the bound ligand TRS and the non-standard nucleotide CBR are both designated part of chain B. Of the 7 water oxygens present in that model, 4 are designated as part of chain A, 2 as chain B, and 1 as chain C.
   
   In the Select Targets for Contacts dialog is a checkbox to include water associated with the target chain as part of the target. When you check this, the Contacts Shown view is no longer cluttered with all the interactions of the target protein chain with its associated water. You will still see interactions of the target chain with other chains, and with water "belonging to" other chains.
   
   When you click on a chain to designate it as a target, if that chain is associated with ligands+ or non-standard residues, you will be asked whether to include them in the target.
   • If you include them, contacts to them will be displayed along with contacts to the standard residues in the chain.
   • If you exclude them, they will be shown as contacting the standard residues in the chain.
   Ligands+ and Non-Standard Residues are listed in the Molecule Information Tab. Clicking on one puts halos around all of its occurrences.
   
   
3. How do I include a subset of the ligands+/non-standard residues in the target? Suppose that you want the non-standard residue CBR in chain B of 1ijw to be part of the target chain B, but you want to exclude the ligand TRS from the target so you can see how it contacts chain B. Since there are only a few entities to deal with, this is easily handled in the target selection dialog using mouse clicks.
   
   Using Mouse Clicks:
   1. One at a time, click on each chain, A, B, and C. When asked whether to include ligands+/non-standard residues, click Cancel to exclude them from the target.
   2. Change the selection mode from Chain to Residues/Groups. Ligands+ and non-standard residues are darker than their chains, as shown in the snapshot at right. Click on the non-standard residue CBR to include it in the target. This leaves the two TRS molecules excluded from the target.
      Now you are ready to Show Atoms Contacting Target.
      
      Alternatively, you could simply target the two TRS Residues/Groups by clicking on them.
   
   Using Find.. & Contacts to "Atoms with Halos":
   • When there are too many ligands+/non-standard residues to target easily by mouse clicks, you can use Find.. to put halos on an arbitrary set of atoms, then, in Select Targets for Contacts check Atoms with Halos.
     
     
   • Generally, if you want to see the contacts between a ligand or non-standard residue and protein, you would not target protein. Instead, to keep the result simple and uncluttered, you would target the ligand or non-standard residue (either by clicking on it, or using Find..).
     
     
   • Suppose you would like to see the inter-chain contacts in a multmeric protein -- but only the protein-protein contacts, not involving ligands or water. Consider 1jyn, a 4-chain protein tetramer with dozens of ligands+ including glycosylation, metal ions, and dimethyl sulfoxide. Limiting the results to protein-protein contacts between chains is best done using Find.. and then targeting Atoms with Halos.
     1. We'll put halos on chain=A as our primary target.
     2. This model has >1,000 waters/chain. If you include all water in the target, the thousands of interactions between the target water and chains B, C and D make a very cluttered result. So you want to include only water in the target chain as part of the target: (water and chain=A).
     3. If you don't want to see contacts between the target chain and its own glycosylation, you need to include the glycosylation of chain A in the target. If you Isolate and check Carbohydrate, you can see that the glycosylation of chain A is chain E. So include chain=E.
     4. Find chain=A or chain=E or (water and chain=A).
     5. In the Select Target for Contacts dialog, check Atoms with Halos. Then click Show Atoms Contacting Target.
     
     Using List Contacts:
   • Regardless of which method you use to select the target, it may be very useful to click List Contacting Atoms and Bonds in the Contacts Shown panel. The list can easily be imported into a spreadsheet for sorting.
   
   
4. Why can’t I deselect by clicking on something already selected? In general, when you selected something by clicking on it, you can deselect it with a second click. For example, if the selection mode is "Chains" and you have already selected Chain A, clicking on Chain A again will deselect it. However, when you are clicking on something that is included in a larger selected set of atoms, it will not be deselected. For example:
   
   
   1. If Chain C is selected, and then you change the selection mode to "Residues/Groups", clicking on a residue in chain C will not deselect that one residue. Solution: To select large portions of a chain, use the "Range of residues in one chain" mode. Alternatively, Find the desired portion(s), for example "chain=B and (1-36 or 58-113)", and then, in the Contacts target selection dialog, check "Atoms with halos".
      
      
   2. If you have selected "Atoms with Halos", and the selection mode is "Residues/Groups", you cannot deselect atoms with halos by clicking on those atoms. Solution: Uncheck "Atoms with Halos". Now, with the selection mode set to "Residues/Groups", use the halos as a guide to click on the subset of groups with halos that you want.
   
   
5. How do I use sequence numbers to target a range of residues? Suppose you want to target the range of sequence numbers 22-33. In the Find.. dialog, enter "22-33" to put halos around the 12 residues from 22 through 33. Now click Contacts... There, check Target Atoms with Halos. Now you are ready to Show Atoms Contacting Target. If there is more than one chain with residues 22-33, for chain B, enter "22-33 and chain=B" in Find...

• Hydrogen bonds (See ~terms for Find..)
  
  Putative hydrogen bonds are reported where nitrogen or oxygen atoms 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 structures 1yjo and 1yjp reported by Nelson et al. (2005) (see Figures rendered in Jmol) were determined not to be such after careful examination of the angles (David Eisenberg, personal communication).
• Water and water bridges.
  
  

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

  In the Contacts Shown display, hydrogen bonds in which one partner is water can be displayed separately from hydrogen bonds in which neither partner is water.
  
  Furthermore, water bridges can be shown separately (a subset of hydrogen bonds involving water). Each bridge includes at least these three atoms:
  1. A target oxygen or nitrogen within 3.5 Å of a non-target water oxygen.
  2. The bridging non-target water oxygen.
  3. A non-target, non-water oxygen or nitrogen within 3.5 Å of the bridging water.
  
  Examples:
  • In 1D66 (Gal4 bound to DNA), protein chain A has a single water bridge, going to DNA. DNA chain D has four water bridges to DNA chain E.
  • In 1BL8, the potassium channel, target any chain in Contacts.. and display only the water bridges. There is a single water in the channel which bridges the four chains. (There are also nice cation-pi interactions between chains.)
  • In 1LCD, numerous waters with hydrogens bridge the protein to the DNA.
• Apolar Van der Waals interactions. (See ~terms for Find..)
  
  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 (See ~terms for Find..)
  
  Sidechain nitrogens (arg.ne,arg.nh?,lys.nz), or N-terminal nitrogens, with a full electronic positive charge at neutral pH within 4.0 Å of sidechain oxygens (asp.od?,glu.oe?) or C-terminal oxygens with a full electronic negative charge at neutral pH. More about salt bridges.
  
  There are two ways to visualize protein salt bridges in FirstGlance: (i) Contacts.. shows them between a target you select and the remainder of the model; (ii) Salt Bridges/Cation-Pi.. (in the Tools tab) enables you to find them throughout the model. Salt bridges where one or both partners is not a standard amino acid are not shown in these views.
  
  
  • Example: Each chain in 2hhd has one salt bridge in each direction between chains A and C. Further examples are described in the lower left (help) panel when you use Salt Bridges/Cation-Pi (Tools tab).
    
    
  • Oxygens missing at carboxy termini: It is fairly common that authors of crystallographic models (PDB files) leave out one of the oxygens on the carboxy termini of protein chains. Such carboxy termini, missing one oxygen, are marked ¶ by FirstGlance in its Ends report (Molecular Information tab or Tools tab). Examples: 1bl8, 2xy9, 1bl8, This is legal according to the PDB format requirements (information from Rachel Kramer Green of RCSB, November, 2017), and the missing oxygen is not listed in REMARK 470 which lists other missing atoms.
    
    When one of the carboxy-terminal oxygens is missing, FirstGlance detects salt bridges by looking for a cationic sidechain within 5.2 Å of the carboxy carbon atom. An example is 5j0z, where the carboxy-terminal Phe315 is salt-bridged to Arg118. When this molecule is processed in FirstGlance’s Salt Bridges/Cation-Pi (Tools tab), the terminal carboxy carbon is represented as a ball to indicate its participation in a salt bridge. In Salt Bridges lower left (help) panel, click "Show halos on: All Protein Chain Termini" to highlight the ends of chains, making it easy to find carboxy-termini engaged in salt bridges. Other examples: 6nie. (Technical: Measurements leading to the choice of 5.2 Å will be found in saltbr.txt. Code is in makeSB_CTermNoOXTCarbonsSpt() in scripts.js.)
  
  
• Salt Bridges vs. Alternate Locations
  
  When FirstGlance is in fewer details mode, no information is provided about alternate locations when they are present. Alternate locations of atoms are hidden in fewer details mode. When you display Salt Bridges (Tools Tab) in fewer details mode, alternate locations involved in salt bridges will not be shown.
  
  When FirstGlance is in more details mode, information about alternate locations (when present in the model) and occupancies is available through links in the Molecule Information Tab.

  Alternate Locations involved in Salt Bridges
  C N O	%A %B  Common

  
  
  When Salt Bridges (Tools Tab) are visualized in More details mode, provided Alternate Locations are not hidden in the Hide.. dialog (Focus Box), alternate locations (when present) involved in salt bridges will be shown.
  Example 7rin:
  
  
  • Glu170.OE1 (sidechain Oxygen Epsilon 1) is within 4.0 Å of both sidechain nitrogens of Arg105%A, but neither sidechain nitrogen of Arg105%B. See snapshots at right.
    
    
  • All of the 4 sidechain oxygens of Glu115 %A and %B are within 4.0 Å of one or more of the 4 sidechain nitrogens of Arg221 %A and %B (not shown).
  
  To color the alternate locations as %A, %B: After displaying the salt bridges, click on alternate locations in the Molecule Information Tab, and there, click only on color alternate conformations.
  
  
• Cation-pi interactions (See ~terms for Find..)
  
  Cationic sidechain nitrogens (lysine or arginine), or cationic protein chain amino-termini, within 6.0 Å of the face of an aromatic ring (phenylalanine, tyrosine, or tryptophan) may engage in polar interactions called "cation pi interactions" (Gallivan & Dougherty, 1999). These play an important role in the overall energetics of protein folding. For a brief introduction, see More about cation-pi interactions.
  
  There are two ways to visualize protein-protein cation-pi interactions in FirstGlance: (i) Contacts.. shows them between a target you select and the remainder of the model; (ii) Salt Bridges/Cation-Pi.. enables you to find them throughout the model. Cation-pi interactions where one or both partners is not a standard amino acid are not shown in these views.
  
  
  • FirstGlance displays putative cation-pi interactions based on the cation being within 6.0 Å of three alternate carbons in an aromatic ring. FirstGlance will fail to show some energetically significant cation-pi interactions, and some that it shows will not be energetically significant. Please see the CaPTURE server for an authoritative listing of sidechain cation-pi interactions.
    
    CaPTURE does not report cation-pi interactions involving cationic amino termini of protein chains, but FirstGlance does display them.
    
    When the model is large, in order to save time, FirstGlance uses a faster but somewhat less accurate method of detection than is used for the smaller 90% of entries in the PDB. The faster method is used for models with >12,000 non-hydrogen atoms, which are the largest ~10% of entries in the PDB. In these cases, the slower method is offered if you wish greater accuracy. An example is 7ahl.
    
    The faster method sometimes shows lysine or arginine without a contacting aromatic ring, or vice versa, and sometimes shows pairs that fail the strict 6.0 Å criterion (see more details in catpi.txt). This is because the faster method looks for three aromatic ring atoms within 6.0 Å of the cation, but cannot tell if the three are in the same ring. The slower, more accurate method applies the 6.0 Å test residue-by-residue.
    
    In the case of 7ahl, initially, four of the six Phe39 residues are shown without associated cations. These disappear after the slower, more accurate method is run.
    
    
  • Neither FirstGlance nor CaPTURE will report cation-pi interactions where the cation or aromatic ring are not standard amino acid components. Examples include metal cations, or aromatic rings in ligands. FirstGlance can, however, show the contacts for any moiety, so you could select metals or ligand aromatic rings, and visualize their contacts.
    
    
  • Examples are provided at the bottom of the lower left help panel when displaying cation-pi interactions. Here are a few more:
    • One end of peptide chain P in 2VAB contains PHE1:P interacting, in an energetically significant manner according to CaPTURE, with LYS66:A.
    • Each chain in the homotetramer 1BL8 has one cation-pi interaction with each of the two chains it contacts. These are deemed energetically significant by CaPTURE.
    • The peptide chain C has one energetically significant cation-pi interaction with chain A in 1B07.
    • Firstglance finds two LYS:PHE cation-pi interactions, one in each direction, between chains B and D in 1IGT. CaPTURE is unable to handle PDB files that contain "inserted" sequence numbers, and this includes 1IGT. However, if the PDB file is renumbered, then uploaded to CaPTURE, results are obtained. CaPTURE deems neither of the proximities detected by FirstGlance as energetically significant.
• Cation-Pi Interactions vs. Alternate Locations
  
  When FirstGlance is in fewer details mode, no information is provided about alternate locations when they are present. Alternate locations of atoms are hidden in fewer details mode. When you display Cation-pi interactions (Tools Tab) in fewer details mode, alternate locations involved in putative cation-pi interactions will not be shown.
  
  When FirstGlance is in more details mode, information about alternate locations (when present in the model) and occupancies is available through links in the Molecule Information Tab.

  Alternate Locations Involved in Cation-Pi Interactions
  C N O	%A %B  Common

  
  
  When putative Cation-Pi Interactions (Tools Tab) are visualized in More details mode, provided Alternate Locations are not hidden in the Hide.. dialog (Focus Box), alternate locations (when present) involved in the putative cation-pi interactions will be shown.
  Example 6b8t:
  
  
  • The cationic sidechain of Arg221 is positioned appropriately to be in a cation-pi interaction with the aromatic rings of Trp179. Alternate locations are specified for both amino acids. See snapshots at right.
  
  To color the alternate locations as %A, %B: After displaying the putative cation-pi interactions, click on alternate locations in the Molecule Information Tab, and there, click only on color alternate conformations.
  
  
• Metal and miscellaneous bonds include several categories of distance-based atom pairs.
  (See ~terms for Find..)
  1. Sulfur atoms within 3.2 Å of a metal atom (presumed to be a cation). "Metal" (Find.. ~metals) is defined as any metal that occured in the Protein Data Bank in February, 2025 (adding actinium (Ac), neodymium (Nd), dysprosium (Dy), plutonium (Pu), americium (Am), and thorium (Th) to the earlier lists from 2013 and 2006), which include the following:
     The following elements did not occur in the Protein Data Bank in February, 2025. Sulfurs interacting with these would not be displayed.
     • francium (Fr).
     • Alkaline earths: radium (Ra).
     • Transition metals: niobium (Nb).
     • Lanthanides: promethium (Pm), thulium (Tm).
     • Actinides: neptunium (Np), protactinium (Pa).
     Elements not listed above were not considered.
     
     
  2. Any atom outside the target that is not (carbon, sulfur, phosphorus, or hydrogen) within 3.5 Å of any atom within the target that is not (carbon, sulfur, or hydrogen); and vice versa. Atoms deemed to be involved in putative hydrogen bonds (see above) are then excluded. The resulting set includes, for example, O-metal, Se-metal, and metal-to-metal interactions, as well as chloride ion interactions with polar moieties, but excludes metal ions interacting with sulfurs.
     
     
  3. Any atom outside the target that is not (carbon, sulfur, phosphorus, or hydrogen) within 3.5 Å of any metal atom within the target; and vice versa. This finds atoms such as nitrogen or oxygen that are probably bound to metals, regardless of whether they may also appear to be involved in hydrogen bonds. The resulting set includes, for example, the sidechain nitrogen in HIS bound to Fe⁺⁺ in heme.
     
     
  4. Any atom outside the target that is not (carbon, oxygen, nitrogen, sulfur, phosphorus, or hydrogen) within 4.5 Å of any atom in the target, or vice versa. This includes, for example, metal or chloride ions interacting with any element, and Se-C or Se-S interactions. This rule is also intended to display interacting elements not anticipated by the preceding rules.
  
  
  Examples (using Contacts..):
  • Targeting either a protein chain in hemoglobin 2HHD, or a heme group, or an iron atom in a heme, shows the histidine sidechain nitrogen interacting with the Fe⁺⁺.
  • Targeting either one cadmium atom or one protein chain in 1D66 reveals the cadmium-sulfur bonds, and the cadmium-cadmium proximity.
  • Targeting the three potassium ions in 1BL8 reveals their bonds to nearby oxygens.
  • Targeting the three potassium ions in 1KF1 reveals their anhydrous bonds to DNA oxygens.
  • 1IXJ includes DNA, water, CoN₆H₁₈ (cobalt hexamine) and MgO₆H₁₂ (magnesium hexahydrate).
    
    

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

• Only models with resolutions of 4.0 Å or better are analyzed. If the PDB file has no header section and therefore the resolution is not known, it is analyzed.
• When alternate locations are present, all conformations are analyzed for possible crosslinks. If the crosslinked residues contain alternate locations, and if FirstGlance is in "Fewer Details" mode (which hides alternate locations), when display of crosslinks is requested (Tools tab), "Show More Details" mode is automatically turned on. This also reports alternate locations and partial occupancies when atoms are touched or clicked. Examples:
  • 1nme.
  • 1jpu.
  • 6zx4 has partial occupancies but no alternate locations.
• Only model 1 is analyzed and displayed (when multiple models are present).
• Criteria are intentionally broad, and will detect some proximities that are not actually the type of bond suggested as putative or possible, often clashes. Thus, detailed examination including the electron density map is crucial. Nevertheless, legitimate bonds will sometimes fail to be detected because they have unrealistically long bonds that fall outside the maxima used by FirstGlance (see examples below).
• Technical: makeFindCrosslinksSpt() in scripts.js. showCrosslinksHelp() in help1.js. showCrosslink() in scripts.js. crosslinkType.
  
  
• CAUTION -- VALIDATION REQUIRED: Models may have clashes that are suggested as putative crosslink bonds, or bond lengths too long to be detected with the cutoff distances used by FirstGlance (see below). This is especially likely for X-ray models with resolutions of 2.5 Å or poorer, models determined by electron microscopy, and models predicted by AlphaFold. Examples of such clashes are given in the lower left (Help) panel for each type of crosslink.
  
  Example of unrealistically long bond lengths: 6nef and 6ef8 are independent electron microscopic determinations of the same protein (outer membrane cytochrome S of Geobacter sulfurreducens). Each heme (HEC) is bonded to 2 cysteines via thioether links. In 6ef8 (nominal resolution 3.7 Å), all such thioether links are detected, with bond links ranging from 1.75 to 2.13 Å. However in 6nef (nominal resolution 3.4 Å), half of the thioethers are detected with bond lengths 1.78-1.86 Å, while the other half are not because they have chemically unrealistic bond lengths 2.54-2.87 Å. The cutoff value utilized is specified below under Thioethers.
  
  
• Bond(?) Clusters. A single protein crosslink is detected between two atoms (N and S for Lys-Cys NOS bonds). When more than two appropriate atoms are within the cutoff distance from each other, it is termed a Bond(?) cluster. FirstGlance does not attempt to specify a single bond. Bond(?) clusters can be visualized using the same tools provided for single-bond atom pairs. Bond(?) clusters usually involve clashes, with the exception of SONOS bonds. Examples of bond clusters:
  • Isopeptides: 3mrm.
  • Thioesters, Thioethers, Esters: No examples identified. If you encounter one, please send the PDB code to
  • His-Tyr: 4rea.
  • Cys-Lys-Cys SONOS: 4ga9 has Cys, Lys, Cys in close proximity. The electron density map supports a SONOS bond in chain A, but not as well in chain B, where the electron density supports only one oxygen. This example is from von Pappenheim et al., 2021.
  
  
  
• Isopeptide crosslinks. Methods:
  1. Lysine sidechain nitrogen (Lys/Dly NZ) within 2.1 Å of a carbon atom that is covalently bonded to a non-water oxygen atom.
  2. Arginine* sidechain nitrogen (Arg/Dar NH?/NE) within 2.1 Å of a carbon atom that is covalently bonded to a non-water oxygen atom.
  3. Any carbon, not in Lys, Arg, Dly, or Dar, that is within 2.1 Å of a nitrogen atom identified in steps 1 or 2 above
  4. For partner carbons identified in step 3 above:
     1. If the partner group is Glu/Gln/Dgl/Dgn, sometimes both CG and CD are within the cutoff distance. Then, CG is ignored. Example: 5VBL.
     2. If the partner group is Asn/Asp/Dsg/Das, perhaps both CB and CG could be within the cutoff distance. Then, CB is ignored. Example: none known.
     3. If the partner group is none of the Gl?/As? family, it is likely a C-terminal residue. Sometimes both C (main chain terminus) and CA are within the cutoff distance. Then, CA is ignored. Example: 7CAP.
  5. Asparagine/Aspartate (Asn/Asp/Das/Dsg) distal sidechain carbon (CG) within 2.1 Å of a nitrogen atom not in the sidechain of Asn/Asp/Das/Dsg/Glu/Gln/Dgl/Dgn.
  6. Glutamine/Glutamate/Pyroglutamate† (Gln/Glu/Dgl/Dgn/PCA) distal sidechain carbon (CD) within 2.1 Å of a nitrogen atom not in the sidechain of Asn/Asp/Das/Dsg/Glu/Gln/Dgl/Dgn.
  7. Any nitrogen, not in a sidechain of Asn/Asp/Das/Dsg/Gln/Glu/Dgl/Dgn, that is within 2.1 Å of a carbon identified in steps 5 or 6 above.
  ⊳ Example: 2xi9. Additional examples are listed in the Lower Left Panel for this example.
  ⊳ Basis for 2.1 Å cutoff: 17 PDB files containing isopeptide bonds have isopeptide bond lengths of 1.3-1.6 Å (resolution average 2.0, range 0.9 - 2.9 Å). A rare outlier, 2x9x (resolution 1.5 Å) has three isopeptide bonds, both according to the publication (Spraggon et al., 2010) and the PDB file (COMPND OTHER_DETAILS). The electron density map confirms these three bonds. However, their isopeptide bond distances are unrealistic at 2.0, 2.2, and 2.9 Å. The cutoff was set to detect some outliers without producing too many spurious "detections". After automated re-refining and rebuilding by PDB-REDO (load 2x9x_redone.pdb), all 3 have typical bond lengths of 1.32-1.34 Å and are reported by FirstGlance.
  ⊳ *No bona-fide examples involving Arginine are known to the However, FirstGlance will report clashes between Arg sidechain nitrogens and carbons in carbonyls as possible isopeptide bonds.
  ⊳ † Pyroglutamate can form by internal cyclization of an N-terminal Glu/Gln. Examples: 2are (Gln1) and 1s1a (PCA1).
  ⊳ Technical: select ~isopeptide_bonds.
  
  
• Thioester crosslinks. Method:
  1. Cysteine sidechain sulfur (Cys/Dcy SG) within 2.3 Å of a carbon atom that is covalently bonded to a non-water oxygen, and is not in Cys or Dcy.
  Example: 2xi9. Additional examples are listed in the Lower Left Panel for this example.
  Technical: select ~thioester_bonds.
  
  
• Thioether crosslinks. Method:
  1. Cysteine sidechain sulfur (Cys/Dcy SG) within 2.3 Å of a carbon atom that is NOT covalently bonded to a non-water oxygen, and is not in Cys or Dcy.
  2. When Cys/Dcy is thioether bonded to carbons CAB/CAC in HEC (heme), sometimes carbon C3C falls within the cutoff distance of 2.3 Å, in which case it is ignored. Example: 6ef8.
  ⊳ Example: 6e87 (sulfur-carbon distance 1.83 Å).
  ⊳ Additional examples are listed in the Lower Left Panel for the above example.
  ⊳ Example with unrealistic bond lengths: 6nef is a cryo-EM model with 6 hemes. There are two thiether bonds to each heme. Half of those bonds (the ones to carbon CAB on each heme) have realistic lengths of 1.78-1.86 Å. The other half (to CAC on each heme) have unrealistically long bonds lengths of 2.54 to 2.87 Å, and those fail to be detected by FirstGlance.
  ⊳ Technical: select ~thioether_bonds.
  ⊳ Basis for 2.3 å cutoff: Although most thioether models have S-C distances of 1.7-1.9 Å, the thioethers Cys93-Tyr157 in 6u4s or 4kwj have sulfur-carbon distances of 2.05 Å. (In 6u4s, PDB-REDO increases it to 2.72 Å.) Therefore, the detection cutoff was relaxed to 2.3 Å. However, some still fail to be detected due to unrealistically long bond lengths (see 6nef above).
  
  
• Ester crosslinks. Method:
  1. Threonine sidechain oxygen (Thr/Dth OG) within 2.1 Å of a carbon atom that is covalently bonded to an oxygen not in (water, Thr or Dth), and that carbon is not in Thr or Dth.
  2. Serine sidechain oxygen (Ser/Dsn OG) within 2.1 Å of a carbon atom that is covalently bonded to an oxygen not in (water, Ser, or Dsn), and that carbon is not in Ser or Dsn.
  3. If the partner group is a C-terminal residue, sometimes both C (main chain terminus) and CA are within the cutoff distance. Then, CA is ignored. Example: 2PNL.
  Ester crosslink example: 4mkm. Additional examples are listed in the Lower Left Panel for this example.
  Technical: select ~ester_bonds.
  
  
• Histidine-tyrosine crosslinks. Method:
  1. Histidine sidechain nitrogen (His or Dhi) within 2.2 Å of a tyrosine (Tyr or Dty) sidechain carbon atom.
  ⊳ Example: 1v54. Additional examples are listed in the Lower Left Panel for this example.
  ⊳ welcomes more examples with His-Tyr crosslinks.
  ⊳ Technical: select ~histyr_bonds.
  ⊳ Basis for cutoff: Although most models with His-Tyr bonds have N-C distances of 1.3-1.7 Å, the distance is 2.05-2.06 Å in 1gge. Therefore, the detection cutoff was relaxed to 2.2 Å.

• Lysine-cysteine NOS crosslinks. Method:
  1. Cysteine sidechain sulfur (Cys/Dcy SG) or sidechain sulfur of S-hydroxycysteine (CSO.SG) within 3.1 Å of a nitrogen atom, which is not a main chain nitrogen, and is in none of Asn/Gln (or their D forms Dsg/Dgn).
  2. The maximum cutoff of 3.1 Å is slightly more generous than the maximum of 3.0 Å used by von Pappenheim et al.. Also, they limited their scan of the PDB to models with resolutions of 2.0 Å or less, while FirstGlance reports S-N proximities in models with resolutions of 4.0 Å or less.
  Example: 6zx4. Additional examples are listed in the Lower Left Panel for this example.
  Technical: select ~NOS_bonds.
  
  Examples with multiple types of crosslinks:
  • 2xi9: isopeptides and thioesters.
  • 2yev: thioethers and His-Tyr.
  • 1nme: thioethers and Lys-Cys NOS with alternate locations.

3 conformations of Arg201 in 7s99, with occupancy percentages.

1. View 3hyd in FirstGlance.
2. If Show More Details is present in the Introduction of in the Molecule Information Tab, click it.
3. Click the link alternate locations in the Molecule Information Tab.
4. Follow the instructions in the lower left panel to animate the two alternate locations for the sidechain of Glu3.
5. Scroll down to the section Background for an introduction.

• 9ins (2 conformations, insulin)
• 7rsa (2 conformations, RNAse)
• 8paz (3 conformations, cupredoxin)
• 8a3h (3 conformations, endoglucanase)
• 1bsz (3 conformations, bacterial peptide deformylase)
• 1dlf (3 conformations, antibody Fv) The sidechain of Asn52 in chain H has alternate locations, and Asn52:H has sequence insertion code A. To Find atoms with alternate locations (%?) and insertion codes (^?), find %? and ^?.

Animation of Ligand: 5 conformations 1 2 3 4 5 of [PO4]201 in the Asymmetric unit of 4nia. Images with only 2 colors are colored by element: O, P. Static images show all conformations at once. To isolate a single PO4, Find [PO4]201 and chain=K, then isolate atoms with halos.

• [GOL]606 (2 conformations) in 8a3h (endoglucanase).
• [TMP]: 4 of the 8 thymidine monophosphates have 2 conformations each in 1fxo (glucose-1-phosphate thymidylyltransferase).
• [8TJ]203 (2 conformations) in 5pog (bromodomain-containing protein 1).
• [USP]2101 (3 conformations) in 5qye (spliceosome assembly factor Aar2 + RNaseH).
• [GOL]200 (5 conformations) in 2qw7 (carboxysome subunit). The 1 and 3 oxygens of this glycerol point in 5 alternative directions.
• [PO4]201 (5 conformations) in the Asymmetric unit of 4nia (see illustrations at right).
• [BCL]900 (6 conformations) chloro-pentafluorobenzene in 3dn1 (T4 lysozyme mutant). The chlorine points in 6 alternative directions.

There were 6,125 PDB entries with ≥ 1.0 Å maximum separation of backbone atoms (alpha carbons or nucleic phosphorus atoms) in May, 2023; 3,560 ≥ 2.0 Å; 1,038 ≥ 5.0 Å. See Alternate locations of backbones.

Alternatively, after applying a schematic backbone view (Secondary Structure, Cartoon, N->C Rainbow, Vines, Thin Backbone) you will see Animate Conformations in the lower left (color key/help) panel. Clicking it applies the conformation color scheme and animates.

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

Loop 174-199 in 4NVK has 4 conformations: 1 2 3 4. N->C Rainbow view colored by conformations.

Color schemes can be preserved during animation of all-atom views (Solid, Composition, Hydrophobic/Polar, Charge, Sticks) by NOT clicking Color alternate conformations before you click Animate the conformations. This might be useful, for example, with the Charge view. When schematic backbone views are animated, conformation coloring is always applied.

Simple
• 1ijw (Protein & DNA. A single DNA backbone phosphate has two alternate locations. Separation is 3.1 Å.)
  
  Two to Seven Conformations
• 7rin (Protein, 16% forked, 2 conformations, max separation 5.9 Å.)
• 6o4f (Protein, 2% forked, 2 conformations, max separation 17 Å. The ~dozen C-terminal residues in chains B and D differ in conformation.)
• 5sop (Protein, 50% forked, 3 conformations, %A%B%C. Max separation of the first two conformations is 11 Å.
• 5e1p (Protein, 76% forked, 4 conformations, %A%B%C%D. Atoms with a single location are marked %A%B%C and %E. Max separation of the first two conformations is 0.6 Å.
• 5i1r (Peptide. When animated, ends (36%) flop dramatically. 5 conformations. Max separation of the first two conformations is 19 Å.)
• 5qye (Protein, 5% forked, 6 conformations, no atoms have 4 or 5 conformations, max separation 0.2 Å.)
• 3b2c (Protein, 100% forked, 7 conformations, %A-%G, max separation 9.6 Å. >6 conformations is quite rare, and FirstGlance 4.2 does not handle the 7th conformation.)
  
  Optional Simplification
• 4aoj (Protein. Optional simplification. If you opt to simplify, alternate location information becomes unavailable. The asymmetric unit has a single Phe with two alternate locations. The two locations for its alpha carbon [the "backbone fork"] are 0.06 Å apart, difficult to distinguish.)
• 4nia (asymmetric unit) (Protein. Optional simplification. If you opt to simplify, alternate location information becomes unavailable. 11% of the alpha carbons have alternate locations, but the max separation is 0.18 Å, difficult to distinguish. 5 conformations.)
  
  Complicated
• 1zir (Crystallin. 3% forked. 2 conformations. Max separation of the first two conformations is 4.5 Å. 22 alternate location markers used, %A-%V.
• 5pog (Protein. 4% forked. 2 conformations. Max separation of the first two conformations is 0.2 Å. Alternate location markers used %A-%C, %E, %F. (No %D in Biological Unit 1 = chain A, but %D in the asymmetric unit, which has 2 chains.)
• 3eoj (asymmetric unit) (Bacteriochlorophyll. 15% forked. 3 conformations. Max separation of the first two conformations is 5.7 Å. Atoms with single locations marked %A and %B. Atoms with two locations marked %A%B, %A%C, %C%D, %E%F. Atoms with 3 locations marked %A%B%C.
• 1cm4 (Protein. 100% of the alpha carbons have 4 alternate locations (4 conformations) coded A,B,C,D. The initial view in FirstGlance shows A & B, where the maximum separation is 7.1 Å. If you click alternate locations in the Molecule Information Tab, and then All Sticks followed by Color alternate conformations, you will see all four in four colors. Due to perhaps a formatting error in the PDB file, calcium alternate locations are given distinct sequence numbers; hence, they are all in conformation 1, so they are all visible even when alternate locations are hidden.)
  
  DNA/RNA
• 3qba (DNA, 30% of phosphorus atoms forked, 2 conformations, max separation 1.7 Å.)
• 7ucr (RNA, 8% of phosphorus atoms forked, 2 conformations, max separation 2.3 Å.)
• 3kqu (Protein + DNA, 100% of DNA phosphorus atoms forked, 4 conformations, max separation 34.4 Å. Shows translocation of single-stranded DNA in a helicase.)
• 1egw (Protein + DNA. All DNA phosphorus atoms have alternate locations. DNA is modeled with each chain in 2 alternate locations (2 conformations), with chains E and F swapping locations in Biological Unit 1. Max separation is 54.1 Å.)
• 3cz3 (Protein + RNA. All RNA phosphorus atoms have alternate locations. Double-stranded RNA is modeled with each chain in 2 alternate locations (2 conformations), with chains E and F swapping locations, and ditto for chains F and G. Max separation is 58.3 Å.)
  
  Singletons
• 3cye (Protein. Mix of alternate locations and Singletons. Good for testing. 42 atoms with 2 locations each plus 13,626 atoms with altloc codes but only a single location/atom.)
• 2gn2 (Protein. Singletons only: 160 protein atoms with altloc codes but only a single location/atom.)
• 1sy7 (Protein. Singletons only: 348 protein atoms with altloc codes but only a single location/atom.)
• 6DLQ (RNA. Singletons only: 22 ligand atoms with altloc codes but only a single location/atom.)
• Further explanation and examples: Alternate locations of backbones (in Proteopedia.org).

1. In order to work with alternate locations, you must be in more details mode. In the Molecule Information Tab, click on Show More Details. (If you see a link Show Fewer Details, then you are already in more-details mode.)
   
   
2. Next, also in the Molecule Information Tab, click on alternate locations. (Gathering the details on alternate locations may take a little time.)
   
   
3. Scroll down in the report (lower left panel) to the bottom of the gray table. There you will see links that isolate atoms with alternate locations:
   
   
   
4. After you have gathered details on alternate locations (step #2 above), you can also isolate them in the Isolate dialog (available from the focus box):

   5sop has 3 conformations. Above, atoms with 3 conformations 1 2 3, isolated. These include 13 alpha carbons (8% of 167 total in conformation 1). Rendered as Vines/Sticks with "more detail" and sidechains hidden. Colored with Color alternate conformations in the alternate locations report.

Alternate Locations in the Contacts & Non-Covalent Interactions Tool
Target in 6B8T: GOL302	Target in 7UCR: G71 and sidechain.
%A %B  Common	C N O  H   Deuterium	%A %B  Common

• 7rin: The ligand TRS402 has alternate locations. You can target one (e.g. %A) or both (%A plus %B) alternate locations. 5 protein atoms contact TRS402%A, while 7 contact TRS402%B. One alternate location of TRS402 contacts the other alternate location of itself, but the one not targeted can be Hidden (Focus box) after the contacts are displayed.
  
  
• 6b8t: Targeting the ligand GOL302 (which has no alternate location) reveals that it is likely hbonded to GLN157.OE1%B (but not %A), ASP148.OD2%A (but not %B), and SER146.OG (which has no alternate location).
  
  
• 7ucr: This is an RNA example. Find G71 and sidechain. Now, request Contacts & Non-Covalent Interactions (Tools Tab) for "Atoms with halos". You will be able to see how G71 interacts with two alternate locations of C49.

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

Clicking on the halos ALL UNUSUAL components or features

1. Single/monomeric amino acids, not part of a polymer. Classified as ligands. Listed under Ligands+ and Non-Standard Residues in the Molecule Information Tab. Examples: 4ffL, 4reo. Find: ~unchained_aas
2. Dipeptides, which are classified as ligands. Listed under Ligands+ and Non-Standard Residues in the Molecule Information Tab. Examples: 4d2c, 1dpp. Find: ~dipeptides
3. D amino acids. Examples: 2soc, 1al4. To hide the D labels, see Labels. Find: ~d_aas
4. Ribothymidine (5-methyl uridine). Examples: 5MU in 1evv and 1i9v. Find: T and RNA
5. Deoxyribouridine. Example: DU in 1g22. Find: U and DNA
   
   Protein Crosslinks:
   The existence of any of the following unusual protein crosslinks triggers an alert, regardless of the preference setting.
   When many atoms have alternate locations, the resulting clashes may cause FirstGlance to suggest crosslinks that are only clashes.
   6. Isopeptide crosslinks. Example: 3htl. Find: ~isopeptide_bonds
   7. Thioester crosslinks. Example: 2xi9. Find: ~thioester_bonds
   8. Thioether crosslinks. Example: 6e87. Find: ~thioether_bonds
   9. Ester crosslinks. Example: 4mkm. Find: ~ester_bonds
   10. Histidine-tyrosine crosslinks. Example: 1v54. Find: ~histyr_bonds
   11. Lysine-cysteine NOS bonds. Example: 6ZX4. Find: ~NOS_bonds

12. GLX or ASX (ambiguous) residues. Example: 1kp0. Find: GLX or ASX
13. Deuterium. Example: 7ucr. Find: deuterium
14. Unknown atoms X, element UNK, group UNX. Examples: 1kp0 (sidechain O/N on ASX, GLX), 5g4a (unknown atoms), 5wbn (unknown atoms). Find: *.x??
15. Unknown amino acids UNK occurring in >1,500 PDB entries. Example: 3hm6 (alpha helix of unknown sequence modeled as poly-alanine). Find: UNK
16. Unknown nucleic residues "N". Examples: in polymer chain, 2i82; not in polymer, asymmetric unit of 3dzi. Find: [n]
17. Unknown ligands "UNL". Examples: 6eqq, Find: UNL
18. Anomalous atoms. Example: none known. Find: ~anomalous_atoms
    
    
19. Amino acids lacking alpha carbon atoms. Example: Thr918 in 1h3o, and Lys214 in 2fd8 have only a nitrogen atom. Arg 475 chain A in 6rt4 lacks several atoms, including its alpha carbon, despite electron density for the main chain. Find: ~nobackbone_aas
20. Amino acids lacking peptide-bonding atoms. Example: Gln8 in 4en3. is missing a main chain nitrogen atom. Find: ~unbondable_aas
21. Amino acids lacking main chain oxygens. Examples: Gly5 in 1b07; Met79 in chain M in 1uc5. Find: ~nomainchaino_aas
    
    
22. Single nucleic acid bases (no ribose, no phosphate) are treated as ordinary ligands, NOT alerted as unusual. Example: Adenine ADE in 1aha.
23. Single nucleoSide (no phosphate), not part of a polymer of standard nucleotides. Examples: A351 in 1bkx; ADN351 in 1fmo. Find: ~unchained_nucleosides
24. Single nucleoTide (has phosphate), not part of a polymer of standard nucleotides. Examples:
    • Adenosine monophosphate (AMP) phosphodiester-bonded to 7BV in 5gyz.
    • Adenosine monophosphate (AMP) bound to Zinc in 5gz5.
    • Adenosine 5' monophosphate (AMP) non-covalently bound to protein in 5udt.
    • Adenosine 2' monophosphate (the common form is 5' phosphorylated) in 5udt.
    • Adenosine diphosphate (ADP) bound to Mg in 6b8b.
    • Adenosine diphosphate (ADP) non-covalently bound to protein in 6bLb.
    • Adenosine 5'-triphosphate (ATP) in 5g4a.
    • Guanosine di- and tri-phosphate (GDP, GTP) non-covalently bound to protein and Mg in 5nd4.
    Find (includes cyclic nucleotides): ~unchained_nucleotides
    or Find: ~unchained_nucleotides and not ~cyclic_nucs
    
    
25. Cyclic nucleotides. Examples:
    • Cyclic-AMP (CMP) non-covalently bound to protein in 5kjx.
    • Cyclic-GMP (PCG) non-covalently bound to protein in 5c8w.
    • 2',3'-cyclic AMP (ACK) in 2ype.
    • Additional examples of cyclic nucleotides.
    Find: ~cyclic_nucs
    
    
26. Insertion codes (see Unusual sequence numbering). Example: 1igy. Find: ^? (^ means the following character is an insertion code; "?" means any insertion code).
27. Zero or negative sequence numbers. Examples: 1d5t, and see others in Unusual sequence numbering. Find: resno < 1

27. When any of the above-listed unusual protein crosslinks are present. (Disulfide bonds are not unusual and their presence is not alerted.) Example: 2xi9.
28. The presence of backbone forks is alerted if FirstGlance is in more details mode. This alert happens regardless of whether the preference Alert for unusual components or features is checked, because an explanation is needed for the backbone forks crosses that are shown in more details mode. Examples. Find conformation 1: ~bbforks1 or find conformation 2: ~bbforks2
29. When protein is modeled with only alpha carbon atoms, or nucleic acid chains are modeled with only backbone phosphorus atoms. Examples: protein in 1a1d, protein and DNA in 1bdx. Find: click on below the molecule.
30. When missing residues are not marked with empty baskets because nearby residues with coordinates (upon which to "hang" the empty baskts) were not found. Example: 4o46.
31. When the number of models given in the NUMMDL record does not agree with the number of conformers submitted in REMARK 210. Example: none known. (Examples found earlier have been corrected by the PDB.)
32. When there are >100 incomplete sidechains. See label S— for examples.

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

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

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

1. Built-In
   Many example PDB IDs are built into FirstGlance:
   1. Views tab: Secondary Structure, Composition, Hydrophobic/Polar, and Charge each list examples (bottom of the lower left "help" panel).
   2. Tools tab: Ends, Disulfides/S/Se, Salt Bridges/Cation-pi (separate groups of examples depending on which view is active), each of the 6 types of Protein Crosslinks, and Crystal Contacts each list examples.
2. The Version History gives numerous examples illustrating new or improved features and bug fixes.
   
   
3. AlphaFold Colab and RoseTTAFold Predictions, Tests for handling predictions, some of which lack header sections.
4. Amino Acids, Counting, Examples.
5. Alternate Locations, Conformations & Backbone Forks, Examples.
6. Amino Acid Ligands (monomers and dipeptides), Examples.
7. Apolar Van der Waals interactions, Examples under Contacting Atoms.
8. Atlas of Macromolecules.
9. Backbone Atoms Only, in Deposited Models, Examples.
10. Biological Units vs. Asymmetric Units, Examples.
11. Biological Units, Color Schemes for Large Assemblies, Examples.
12. Carbohydrate and Non-Standard Residue Chains and Water, Examples.
13. Cation-Pi Interactions, Additional Examples under Contacting Atoms.
14. Caveats specified by the authors, cases illustrating.
15. Chains & Chain Details, Test Cases for Finding.
16. ConSurf Server Results: Visualizing in FirstGlance, Examples.
17. Crosslink Detection Methods, Examples.
18. D-Amino Acid Examples.
19. Electron Density Maps, Test Cases.
20. Error Handling Tests in the section Model Data Files Compatible.
21. Gallery of Interactive Macromolecules: use link at the Main Entrance to FirstGlance.
22. Incomplete Sidechains (or Incomplete Nucleotide Bases): S- Examples.
23. Information about the material studied, additional (REMARK 400) specified by the authors, cases illustrating.
24. Ligands+ Examples.
25. Metal & Miscellaneous Bonds, Examples under Contacting Atoms.
26. Nucleic Residues, Unknown "N", Examples'.
27. Nucleotides, Counting: P vs. C5, Examples'.
28. Related PDB Files (REMARK 900) specified by the authors, cases illustrating.
29. Salt Bridges, Additional Examples under Contacting Atoms.
30. Sequence differences between the model and UniProt (SEQADV), Examples.
31. Sequence remarks by the authors (REMARK 999), cases illustrating.
32. Simplification of ConSurf Results, Examples.
33. Simplification of Large Models illustrating model sizes that trigger different levels of simplification.
34. Simplified/Fewer Details Mode: Cases illustrating information hidden in that mode.
35. Status of a PDB code, testing, such as unassigned, withdrawn, obsolete, or on hold.
36. Unusual Components or Features, Examples.
37. Water & Water Bridges, Examples under Contacting Atoms.

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