AIB KUBASIK JMOL FULL
AIB KUBASIK JMOL PLUS
AIB KUBASIK JMOL SERIES

AIB KUBASIK JMOL SERIES

A 'polymer' is a series of connected 'monomers' (at least for these purposes). The coloring operates independently for each chain.Ī variation, relating to 'monomers' in a 'polymer' rather than 'groups' in a 'chain'.The order of groups in the file is used, not the number assigned.Groups in the chain (that is, the scale is relative, not absolute).

AIB KUBASIK JMOL FULL

The full color range is applied across the specified or selected.(red = oxygen = C-terminal = end of chain = 3') (blue = nitrogen = N-terminal = start of chain = 5') To position of the corresponding groups or residues (for example,Īmino acids or nucleotides) along a chain. Related commands: color group, color monomerĪ reverse rainbow gradient (bgyor) is used to color according Red -> tints of red-pink -> white -> tints of blue -> blue Blue-white-red gradient (bwr)īlue -> tints of blue -> white -> tints of pink-red -> red Low rainbow Red -> orange -> yellow -> green -> blue Reverse rainbow (bgyor)īlue -> green -> yellow -> orange -> red Red-white-blue gradient (rwb) In these cases, several color gradients or 'rainbows' are used by Jmol. Several properties that adopt a continuous range of values can be used to color atoms and structures. (HELIX and SHEET records), if available, or determined using an algorithm. The secondary structure is either read from the PDB file Structures (three types of helices, beta strands or sheets, turns, and loops) andĭNA vs. Uses different colors to distinguish six types of protein secondary They may be selected independently (see the Although chain 'A' is the same color as chain 'a' (and so forth), punctuation characters) but this is no longer Remediation of the database may have chain IDs that are blank or notĪlphanumeric (e.g.

AIB KUBASIK JMOL PLUS

(26 times 2, for upper and lower case letters A-Z, plus 10, for chain IDs 0-9).Īn example with 62 chains is 2zkr. Maximum of 62 chains is permitted in a single model within a PDB file That each chain ID be a non-blank alphanumeric character. Than those in ATOM records: darker for chains A-Q,S, lighter for chains R,T-Z. Of a multimeric structure or the individual DNA strands of a double helix.Ītoms in HETERO groups (PDB files only) are colored in a different shade This color scheme is particularly useful for distinguishing the parts Renders each chain in the structure in a different color. (each one different) and also colors differentially the 6 kinds 'shapely' uses a different set of colors for amino acids Some colors are shared by two or more amino acids with similar properties. (as well as Asx and Glx) in a certain color,Īlong with one additional color for anything else (including nucleotides, solvents, and non-amino ligands). 'amino' renders each of the 20 standard amino acid residues Related commands: color amino, color shapely (or later) only differences with classic CPK are shown.īut has been omitted for clarity in the table. Hover over any element to see more information.Ĭlick on an element to move to the same information in the Atomic Numbers table below.ĭefault element colors, by atomic number: “CPKnew” scheme applies only to Rasmol v. Default element colors, by periodic table:

are rendered in the color of alpha carbons for proteins, phosphorus for nucleic acids. Backbone displays such as ribbons, cartoons, etc. Atoms ('CPK' colors, default element colors)Ĭolor cpk, set defaultColors Jmol, set defaultColors RasmolĪpplies color to each atom of the object according to element, as shown in the tables below. Many of the following coloring patterns apply only to PDB and mmCIF files for biomacromolecules. Information on RasMol colors is included for those who are adapting RasMol and Chime-based materials for use in Jmol. if the object is omitted, atoms is assumed.can be atoms, bonds, backbone, cartoon, stars, rockets, ribbon, dots, label, echo, hbonds, ssbonds, axes, boundbox, measures, polyhedra, isosurface, pmesh, unitcell.is specified using pre-defined terms detailed on this page.(For the default colors and color values used in Jmol, see tables below.) It can also be a JavaScript color name, a RasMol color name, or a Jmol color name. is specified as decimal or hexadecimal triplets.Objects can be custom colored in Jmol using the color (or colour) command: Atoms ('CPK' colors, default element colors).

Aib kubasik jmol