Biological unit: The major functional quaternary structure of a molecule.Īlso called the "biological assembly", "biomolecule", or "specific oligomer".Biological assembly: See Biological Unit.Beta strands/sheets: See Secondary Structure.(non-glycine) amino acids is shown in the Beta carbons, missing: A count of the number of beta-carbons missing from.Background color, black or white: The background color toggle button is the second square button in the.Smoothed ribbon representations of the backbone can be seen in Secondary Structure and Cartoon (Views tab). Smoothed backbone traces can be seen in N->C Rainbow (Views tab). Jagged backbone traces can be seen in the Vines and Thin Backbone Views. Backbone trace: For proteins, a backbone trace is a line following the positions of alpha carbons (see backbone representations).Axes for atomic coordinates: The Cartesian coordinate axes can be displayed: use Advanced/Technical in the Tools tab.The APD is the average number of replacements between any two sequences in the MSA.Ī distance of 1.0% means that, on average, the observed replacement for every 100 sequence Average Pairwise Distance (APD): The APD is a measure of the diversity of sequencesĬonSurf reports the APD to characterize the MSA used for calculating conservation levels.Authors: Authors of the model are listed in theīelow this list are links to show the abstract of the structure report, and other relevant citations provided in the PDB file.Near the bottom of each explanation is a list H/non-H Atom Counts by Composition. If you click on elements, you'll get a count of each chemical element. Under "Asymmetric Unit" are reports of chemical elements, and hydrogen in the model.Ĭlick on either link to get a more detailed report. Atom counts: To get counts of all atoms in a model, open the.Assessment plans for educators: See Plans.Assembly, biological: See Biological Unit.To hide these or change the rendering (or for examples), use Advanced/Technical in the Tools tab. Anomalous atoms: Atoms shown as dots in the initial view are "anomalous atoms" that do not fit the format standards for a Protein Data Bank data file.The built-in method (see Animations) is unsatisfactory. Animation Kit: An alternative method for making presentation-ready animations when.In presentations (Powerpoint, Google Slides, Libre Office, etc.). These animations (multi-GIFs) can be shown (highlighted in orange) below the molecule. Animations: To save an animation, click "Save Image or Animation".Angles: Use Distances/Angles in the Tools tab.Amino acids, total number in the model: Given as a count of alpha carbon atoms in the.Or lacking peptide-bonding atoms, or lacking main chain oxygens Amino acids, monomeric (not part of a polypeptide), or lacking alpha carbon atoms,.Amino acid, locating in the molecular view: See Find.In "fewer details" mode, alternate locations are not shown in any view, and the checkbox See also "%A, %B, etc." at the top of this section.Īlternate Locations can be hidden in the Hide dialog (Focus box). You can animate alternate conformations, and find various subsets.
#JMOL FIRST GLANCE CODE#
You will see a table analyzing alternate locations, including the actual number of locationsįor each atom that has an alternate location code (locations/atom).
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