Examples demonstrating how to center, translate, rotate, place a molecule

(For a full list of functions that can move around molecules, go to List_build_functions or the List_general_functions)

Contents

First set some convenient matlab settings

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

Pick filenames to import and export

Set some filenames

filename_in='Ethanol.pdb'; % default is 'Pyrophyllite.pdb'
filename_out='outEthanol'; % default is 'test'

First import some molecule

atom=import_atom(filename_in);

Note that you can issue plot_atom(atom,Box_dim) or vmd(atom,Box_dim) (if VMD is installed and Matlab knows the path to it) to see the molecule

Center a molecule

Use center_atom to center the molecule in the middle of the box. Note that you could pass two additional arguments that can be used to center only a specific resname (molecule name) and/or along specific x|y|z dimensions. Look for instance into center_atom and examples 2 and 3.

centered_atom=center_atom(atom,Box_dim);
% plot_atom(centered_atom,Box_dim) % Run command to see what changed

Translate a molecule

Use translate_atom to translate the molecule somewhere. Note that you could pass one additional argument that can be used to translate only a specific resname (molecule name). Look for instance into translate_atom and examples 2 and 3.

translated_atom=translate_atom(atom,[0 5 10]);
% plot_atom(translated_atom,Box_dim) % Run command to see what changed

Place a molecule

Use place_atom to place a molecule somewhere Note that the place_atom function is dependent on the COM_atom function and is therefore a bit slow for large molecules

placed_atom=place_atom(atom,[0 5 10]);
% plot_atom(placed_atom,Box_dim) % Run command to see what changed

Rotate a molecule

Use rotate_atom to rotate the molecule. The second argument can either be the string 'random' or a 1x3 array holding the new rotation angles around the x,y,z axes. Note that the rotate_atom function is dependent on the COM_atom function and is therefore a bit slow for large molecules

rotated_atom=rotate_atom(atom,Box_dim,'random');
% or to rotate with specified angles around the x,y,z axes.
rotated_atom=rotate_atom(atom,Box_dim,[0 90 180]);
% plot_atom(rotated_atom,Box_dim) % Run command to see what changed

Published with MATLAB® R2022a