How to define selections

The LovoAlign Sever uses VMD in background to define the selections. Therefore, the selections can use the powerful syntax of VMD. Some examples are given below, and references to the VMD user guide are provided for more advanced usage.

Here are some illustrative examples can quickly introduce the user to the VMD selection syntax.

1.	Select only Cα atoms:
	name CA
2.	Select only Cα atoms belonging to Arginines:
	name CA and resname ARG
3.	Select the backbone:
	name CA N CB
3.	Select only the backbone of chain B:
	chain B and (name CA N CB)
4.	Select the HEME group:
	resname HEME
5.	Select only the atoms 5. Å from the HEME group:
	within 5. of resname HEME

Acknowledgements to VMD:

VMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.

VMD references:
Humphrey, W., Dalke, A. and Schulten, K., `VMD -Visual Molecular Dynamics', J. Molecular Graphics, 1996, vol. 14, pp. 33-38.
http://www.ks.uiuc.edu/Research/vmd/