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| 1 | +#show_ligand_interactions v.1.0 |
| 2 | +# author: Thomas Evangelidis, 2019 |
| 3 | +# License: BSD-2-Clause |
| 4 | + |
| 5 | +from pymol import cmd, util |
| 6 | + |
| 7 | +def show_ligand_interactions(recsel="not hetatm", ligsel="hetatm", cutoff=5): |
| 8 | + """ |
| 9 | +DESCRIPTION |
| 10 | +
|
| 11 | + Visualize interactions between receptor and ligand. |
| 12 | +
|
| 13 | +ARGUMENTS |
| 14 | +
|
| 15 | + recsel = string: atom selection of the receptor {default: "not hetatm"} |
| 16 | +
|
| 17 | + ligsel = string: atom selections of the ligand {default: "hetatm"} |
| 18 | +
|
| 19 | + cutoff = float: show as sticks all receptor residues within this distance from the ligand {default: 5.0} |
| 20 | + """ |
| 21 | + cmd.select('ligand', ligsel) |
| 22 | + cmd.select('receptor', recsel) |
| 23 | + cmd.bg_color('white') |
| 24 | + cmd.show_as('cartoon') |
| 25 | + cmd.show_as('sticks', 'hetatm') |
| 26 | + cmd.set('cartoon_transparency', 0.2) |
| 27 | + cmd.spectrum(selection=recsel+" or "+ligsel,byres=1) |
| 28 | + util.cbag('not elem C') |
| 29 | + cmd.set('cartoon_fancy_helices', 1); |
| 30 | + cmd.show("sticks", "(hydro)"); |
| 31 | + cmd.select("pocket", "byres (receptor within %s of ligand)" % cutoff); |
| 32 | + cmd.show("sticks", "pocket") |
| 33 | + cmd.hide('(h. and (e. c extend 1))') |
| 34 | + cmd.set('h_bond_max_angle', 30) |
| 35 | + cmd.set('h_bond_cutoff_center', 3.6) |
| 36 | + cmd.set('h_bond_cutoff_edge', 3.2) |
| 37 | + cmd.dist('ligand_Hbonds', 'ligand', 'receptor', 3.5, mode=2) |
| 38 | + cmd.set('dash_radius', 0.15) |
| 39 | + # now set the label options |
| 40 | + cmd.set('label_size', 20) |
| 41 | + cmd.set('label_position', [0,0,10]) |
| 42 | + |
| 43 | +cmd.extend('show_ligand_interactions', show_ligand_interactions) |
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