Examples demonstrating how to plot the atom struct

(See also the list List_general_functions)

Contents

First set some convenient matlab settings

format compact; set(gcf,'Visible','on');

Pick filenames to import and plot

Set some filenames

filename_in='Pyrophyllite.pdb'; % default example is 'Pyrophyllite.pdb'

Import some molecule

atom=import_atom(filename_in);
% atom=replicate_atom(atom,Box_dim,[4 2 1]) % Replicate the molecule just to get a bigger system

Plot using vmd

The vmd function is basically a redirect to the popular VMD molecular visualization software, that must be installed separately. Hence look into the vmd function and set the path to VMD so Matlab can find it. Typically on a Mac it looks something like this:

PATH2VMD = '/Applications/VMD\ 1.9.2.app/Contents/MacOS/startup.command';

The vmd function can take the structure filename as input, or the atom variable, and/or the Box_dim variable as input.

Examples

vmd(filename_in)
vmd(atom)
vmd(atom,Box_dim)

Plot using show_atom

The show_atom function is a really slow viewer function that can show the atom struct in a coordinate system using the different representations:

Examples

Examples

show_atom(atom)
show_atom(atom,Box_dim)
show_atom(atom,Box_dim,'vdw') % representation style, should be either 'ballstick' (default),'licorice','halfvdw','vdw', 'crystal', 'lines', 'labels' or 'index'
show_atom(atom,Box_dim,'ballstick',1) % Will show the unit cell/box
show_atom(atom,Box_dim,'ballstick',0,0.3) % Will use 30% transparency
show_atom(atom,Box_dim,'ballstick',0,0,[0 0 -50]) % Will translate the XYZ coordinates
show_atom(atom,Box_dim,'ballstick',0,0,[],[0.5 0.5 0.5]) % Single color as given by the 1x3 RGB vector

Plot using show_density_atom

The show_density_atom function is a really simplistic viewer function that can show the atom struct in a coordinate system, along with density profiles that has been smoothed through a Gaussian convolution. Note that the system is wrapped before calculating the density profiles.

Examples

show_density_atom(atom,Box_dim)
show_density_atom(atom,Box_dim,2) % 2 is a scale factor for the plotted atoms
show_density_atom(atom,Box_dim,1,3) % Here the second argument 3 scales the plotted density profiles

Plot using plot_atom

The plot_atom function is a really simplistic viewer function that can show the atom struct in a coordinate system. If first invoking the bond_angle_atom function generating the Bond_index variable, all bonds (also across the PBC) can be plotted if supplying the Bond_index variable.

Examples

plot_atom(atom,Box_dim)
plot_atom(atom,Box_dim,2) % 2 is a scale factor for the plotted atoms
plot_atom(atom,Box_dim,1,Bond_index) % Bond_index from bond_angle_atom()
plot_atom(atom,Box_dim,1,[],'axis') % Will show an axis in the lower left corner

Plot using plot_density_atom

The plot_density_atom function is a really simplistic viewer function that can show the atom struct in a coordinate system, along with density profiles that has been smoothed through a Gaussian convolution. Note that the system is wrapped before calculating the density profiles.

Examples

plot_density_atom(atom,Box_dim)
plot_density_atom(atom,Box_dim,2) % 2 is a scale factor for the plotted atoms
plot_density_atom(atom,Box_dim,1,3) % Here the second argument 3 scales the plotted density profiles

Published with MATLAB® R2022a