A VMD plugin to simplify setting the view direction, and to draw crystallographic vectors
Tcl
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
samples
.gitignore
README.markdown
crystallography.tcl
crystallography_gui.tcl
pkgIndex.tcl

README.markdown

About

VMD plugin written primarily to make it easier to align the view direction along specific crystallographic directions. It also includes commands to convert vectors between crystallographic and cartesian coordinates, and to draw arrows indicating the crystallographic axes arrows and/or the current view direction.

The plugin can be used either from the command line or from a GUI, inspired in part by the "Orientation" window of the program VESTA and the "Set View Direction" window of CrystalMaker.

For the plugin to work, the loaded molecule must contain unit cell information. If VMD can not read this from your file, it can be set manually using the pbctools plugin. Note that pbctools also provide the nice command `pbc box' to draw the unit cell.

Installation

Put the crystallography folder in a folder searched by VMD, that is, a folder listed in auto_path. For instance, you may put it in ~/vmd/plugins, and add

set auto_path [concat "{$env(HOME)/vmd/plugins}" $auto_path] ;

to your ~/.vmdrc (or vmd.rc' on Windows) file. To add the plugin to the Plugins-menu, add the following to your~/.vmdrc` file (or just type it in VMD when needed):

vmd_install_extension crystallography cryst_tk "Crystallography"

Example usage

To view along the [111] direction, type view_along {1 1 1} (list notation) or view_along 111 (short-hand notation) To view towards the (100) plane, type view_towards {1 0 0} or view_towards 100. To show crystal axes, type crystal_axes on -position lower-left, say. Similarly, type view_vectors on to show the vectors of the current viewing plane. The plugin tries to show these as properly formatted Miller indices when a crystal plane is in focus.

The commands cart2dir and cart2rec transforms a vector from a cartesian basis {i,j,k} to a real space lattice basis {a,b,c} and a reciprocal space lattice basis {a*,b*,c*}, respectively. And dir2cart and rec2cart transforms the other way around.

All the above can also be carried out using the GUI, that can be opened by using the menu item or by typing cryst_tk.

See crystallography.tcl for more information.

Vector drawing

GUI

The font rendering on Linux is probably better if VMD is built with Tcl 8.5 instead of 8.4. Seems to be encoding issues on Windows.

GUI on Mac OS X

GUI on Linux/Gnome

GUI on Windows XP