![]() Then to use it, open Jmol application, open menu "Macros", and there you will have a "Ball & Stick" entry. (the full script must go in a single line)Īnd save as ballandstick.macro (or the name you like) in the folder $HOME/.jmol/macros Script=select all color cpk wireframe only wireframe 0.15 spacefill 23% ![]() To show everything as balls-and-sticks in CPK color, create a text file with this contents: (feel free to add your own) Balls & sticks Note that macros will be listed in the Jmol application Macros menu alphabetically by file name, not by title. The macro file must be a text file with the extension macro, and itsĬontents must be two lines, starting respectively with "Title=" and "Script=" (only one macro per file). My PC > right-click > Properties > Advanced Options (tab) > Environment Variables (button) or open a command line and type set Windows: the $HOME folder's location is stored in the environment variable %USERPROFILE% or in the environment variables %HOMEDRIVE% and %HOMEPATH% it will usually be atĬ:\Documents and Settings\(yourUserName)\ ![]() It will show up in the Macro menu of the Jmol application. It is saved as a simple text file, like any other script, in the $HOME/.jmol/macros subdirectory. Introduction to macros in Jmol applicationĪ Jmol macro is a small script that provides some reusable functionality for the Jmol Application. 2.3 Color according to DRuMS MacroMicro scheme.1 Introduction to macros in Jmol application.Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors.To show a vertical/horizontal color bar indiacting the b-factor variation, use the script pseudobar.pml on the structure pseudobar.pdb, or do the following: Spectrum b, blue_white_red, minimum=20, maximum=50 B-factor coloring can be done with the spectrum command. Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2, define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).1 Home Demonstration pages Websites Documentation Wiki History FAQs Browser check Download Project pages Colors Jmol colors Atoms ('CPK' colors, default element colors) Residues: amino acids, nucleotides Chains Secondary structure Gradients Position along chain Positional Variability Charge Isosurfaces Hydrogen bonds Sources JavaScript colors Netscape 8 bit color palette Jmol colors Objects can be custom colored in Jmol using the color (or colour) command: color is specified as decimal or hexadecimal triplets.īe sure that CA's are separated by a contant value, say 5 Angstroem.It can also be a JavaScript color name, a RasMol color name, or a Jmol color name. (For the default colors and color values used in Jmol, see tables below.) is specified using pre-defined terms detailed on this page. can be atoms, bonds, backbone, cartoon, stars, rockets, ribbon, dots, label, echo, hbonds, ssbonds, axes, boundbox, measures, polyhedra, isosurface, pmesh, unitcell. if the object is omitted, atoms is assumed Information on RasMol colors is included for those who are adapting RasMol and Chime-based materials for use in Jmol. Many of the following coloring patterns apply only to PDB and mmcif files for biomacromolecules. Atoms ('CPK' colors, default element colors) Related commands: color cpk, set defaultcolors Jmol, set defaultcolors Rasmol Applies color to each atom of the object according to element, as shown in the tables below. Backbone displays such as ribbons, cartoons, etc. are rendered in the color of alpha carbons for proteins, phosphorus for nucleic acids. Click on an element to move to the same information in the Atomic Numbers table below.ĭefault element colors, by periodic table: Hover over any element to see more information. H Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba L* Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn He 1 of 14 2/15/10 10:12 AMĢ Fr Ra A* Rf Db Sg Bh Hs Mt (L:) La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu (A:) Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr Default element colors, by atomic number: CPKnew scheme applies only to Rasmol v (or later) only differences with classic CPK are shown.
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