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What is hom and het?

Updated: 4/28/2022
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Hom means homogeneous. This is when the element is the same throughout. Het means heterogeneous and this means that the content of an element varies or is a mixture of things.

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What are the signs of an exothermic reaction?

The reaction vessel will warm/hot to the touch. 'Exothermic' ; het coming out. Conversely, if the reaction vessel feels cool/cold to the touch it is Endothermic ; taking in heat from its surroundings.


What type of atoms are in the color yellow?

Atoms may be specified in commands using: * hierarchical specifiers * zones * built-in classifications * attributes or combinations of these. Some commands also accept specifications of nonatomic models. When a plus sign (+) has been typed into the Command Line, it will be replaced by the atom specification string of the next picked atom. Each plus sign must be preceded and followed by a space (or the end of the line). In addition, the following are valid atom specifications: * selected, sel, or picked, indicating atoms that are selected * names of previously saved selections, using sel=selection_name or just selection_name; if a saved selection has the same name as a surface category, the saved selection will be used. Those familiar with atom specification in Midas may wish to consult the summary of differences. {| ! colspan="3" | BASIC ATOM SPECIFICATION ! Symbol ! Reference Level ! Definition | #model number assigned to the model by default or by the user with the open command. :residue residue nameORresidue sequence number, with any insertion code appended ::residue residue name @atom atom name Each file of coordinates opened in Chimera becomes a model with an associated model ID number. Model numbers are assigned by the user with the open command or sequentially by default. Each model contains one or more residues, and each residue contains one or more atoms with names that are unique within that residue. Thus, an atom can be specified by its model number, residue number, and atom name. The lack of a specifier is interpreted to mean all units of the associated reference level; for example, if a model number is not given, the specification refers to all models. Residue and atom names are read from the input file. In PDB format, a standard nomenclature is used for standard amino acid and nucleic acid residues. Asterisks (*) in input atom names will be translated to prime symbols ('), but translated back if coordinates are later saved to a file. Prime symbols in input atom names are not translated on input or output. Model and residue numbers are integers, although a residue number may have an insertion code directly appended. Multiple model numbers or residue numbers may be indicated by comma-separated lists and/or one or more ranges of the form start-end. The words start and end can be substituted for start and end, respectively, and all can be substituted for the whole range (same as no specification at that level). Residue names and numbers cannot be specified together using a single colon, but both can be specified in a single line by using more than one colon. For example, :hem:52 (NOT :hem,52) specifies all residues named HEM and residue 52. In some cases, the basic notations cannot uniquely specify the model, residue, or atom of interest: ! colspan="2" | SUBCATEGORIES ! General Form ! Explanation | #model(s).submodel(s) when a single PDB file contains multiple MODELs, they are considered submodels 1, 2, ... of a single model in Chimera :residue(s).chain(s) when a single model contains multiple chains, a unique specification includes both residue number and chain identifier @atom(s).altloc(s) when a single residue contains alternate locations of certain atoms, an independent specification includes both atom name and alternate location identifier Submodel(s) are integers and may be indicated by a single value or a range of the form start-end. The words start and end can be substituted for start and end, respectively, and all can be substituted for the whole range (same as no submodel specification). Chain(s) and altloc(s) are alphabetical characters. Any residue in PDB HETATM records (or the mmCIF equivalent) that does not already have a chain identifier is assigned to chain het, unless the residue is named WAT or HOH, in which case it is assigned to chain water; residue numbers are unchanged. (See also the residue attribute isHet.) Capitalization of residue and atom names, chain identifiers, insertion codes, or alternate location identifiers is not important, with one exception: when a model contains both uppercase and lowercase chain identifiers, case matters for chain specification in that model only. Subcategorizations are appended to the basic specification. The symbol for the relevant category (#, :, or @) must precede the subcategory specification, although they need not be immediately adjacent. Because commas are used only to separate values of the basic reference levels (model, residue, and atom), they cannot be used to separate values of the sublevels directly. For example, #0.1-3,5 is interpreted as submodels 1-3 of model 0 and all of model 5, while #0.1-3,.5 indicates submodels 1-3 of model 0 and submodel 5 of all models. A subcategory specification applies only to the preceding category value(s) not separated from it by any commas. Thus, :50.B,.D indicates residue 50 in chain B and all residues in chain D; :12-15,26-28.a,45.b@caspecifies CA atoms in residues 12-15 in all chains (except the special chains het and water), 26-28 in chain A, and 45 in chain B. The following specifies residues 12-15 in no-ID chains only: :12-15. Additional examples: #0 - all atoms in model 0 :.A@ca,c,n,o - peptide backbone atoms in chain A :522.water - water residue 522 (a HETATM residue named HOH or WAT without a chain ID in the input file) :lys- or -::lys - all lysine residues #3:45-83,90-98 - residues 45-83 and 90-98 in model 3 #0:12@CA@N - alpha carbon and nitrogen of residue 12 in model 0 (in that order) #0:12@CA,N - alpha carbon and nitrogen of residue 12 in model 0 (unordered) Using the @ notation for both atoms specifies their order (important for certain commands, such as match). Using commas specifies a "group" of atoms, in no particular order. Groups of residues (models) are specified analogously. :12,14@CA - alpha carbons of residues 12 and 14 :12:14@CA - all atoms of residue 12 and alpha carbon of residue 14 :12-20@CA:14@N - alpha carbons of residues 12-20 and nitrogen of residue 14 WILD CARDS The global wild card * matches all atoms in a residue or all residues in a model. 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