Show polar interaction#
- Select the ligand in the model and rename the object to 'ligand'.
- Select the ligand,
actions->around->residues within 5 angstrom, rename the selected object to 'active', show the residues as sticks. - Find the polar interaction:
action->find->polar contacts->to other atoms in object. - Some dashed may connect to the blank space, this may caused by hidden water. Show the water within 3.2 angstrom(hydrogen bond is less than 3.2 angstrom) with
select $LigandWater, (($ligand)around 3.2) and(resn HOH), then a object named '$LigandWater' is generated.
Export#
- Click the middle button of the mouse on the atom to set it as the center, rotate to the proper angle to show the interaction.
- Display the background with white:
Display->background->white. - Click Draw/Ray, set to 300 DPI, click ray.
- Remove the shadow if you like:
setting->Rendering->shadows->None
Reference#
此文由 Mix Space 同步更新至 xLog
原始链接为 https://xxu.do/posts/academic/Demonstate-polar-interaction-between-protein-and-ligand-in-pymol