#VMD TK CONSOLE COMMANDS CODE#

Typically you can play around with these options using the graphical interface, identify those you like and then hard code them into the script. First we define that format we want, in this case I have specified particular settings for the CPK representation, these are the sphere_scale then bond_radius then sphere_resolution then bond_resolution. now we want to add a new representation of this molecule in the CPK format.in VMD anything to do with the molecule is via the 'mol' keyword, in this case we want to read in and display a new moleule and the input file type is xyz.Typically a black background is good for on-screen but if you want to put a snapshot image in a presentation a ligher background works better.Ĭolor Display Background iceblue ::set the background colourĭisplay projection Orthographic ::all atoms same size=orthographicĭisplay depthcue off ::turn off the depth shading We didn't set the background in the script above, but you can alter your script to do this by adding the background command. VMD sets some default options that are not optimal for viewing molecules, for example the default representation is lines, which is very difficult to see, so I typically change these default options in the first part of the.Where atom can be the atomic symbol or atomic number, and you must have as many atom x y z lines as you have number of atoms

VMD can read in many types of format, but an easy option is to just produce the basic xyz file, this has the following format.now that you have made a script loaded and played it, lets discuss in a bit more detail what the format of the input file is and what this script does.a molecule of methane should appear in the VMD window.in this case open VMD, make sure you are in the directory that contains these files by using the 'cd' command, then type into the VMD console source load.tcl then load.we also need a molecule to load, so copy the methane geometry file below into a file called methane.xyz.# change the molecule representation so we can see it Copy this script into a file called load.tcl now you should have a go at doing this, the following is a very simple script called load which sets some display options, loads a molecule input file (methane.xyz) into the VMD viewer, and then displays it using the CPK (balls and sticks) representation.This is achieved by typing in the vmd console source script.tcl then procedure name the general method is that you start by 'loading' the Tcl script file (only done once) and then 'playing' the procedure (as many times as you want).a script is a file ( filename.tcl) which contains a procedure or 'proc' which is a list of instructions for vmd.Basic: using a script to load a molecule introduction

Vmd tk console commands