Usage with a single topology file

If you want to have a look at a single topology file - a docked pose or a frame from simulation - it is easily done with LINTools. Since LINTools uses MDAnalysis to support importing of files, any filetype [supported by MDAnalysis] (https://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/init.html#id1) can be imported by LINTools as well. In these examples, a [PDB] (http://www.rcsb.org/pdb/explore.do?structureId=4XP1) file is used.

The simplest case requires just the topology file and an output filename

lintools -t 4XP1.pdb  -o my_ligand_pic

This input will provide you with a selection of ligands that can be analysed:

# Nr  # Name   # Resnumber  # Chain ID
0 MAL 704 A
1 MAL 705 A
2 NAG 706 A
3 P4G 707 A
4 LDP 708 A
5 EDO 709 A
6 Y01 710 A
7 CLR 711 A
Choose a ligand to analyse: 

In this case 4 (LDP) was selected. Once that is done, the next option is presented:

1  :  amino
2  :  domains
3  :  clock
Choose diagram type: 

After entering 1, LINTools will start working on your picture by detecting hydrogen bonds and deciding where to put residues that are close by. Once everything is plotted and an image is assembled, you will be notified. (It should only take a couple of seconds though, so no coffee time). Of course, you can try the other options as well.