Jayden

Intro#

You can demostrate the pi-pi interaction with wizard->measurement->Distances to Rings, it's easy to do and there's no need to hide the pseudoatom.

However, when demostrate the pi-cation interaction, Distances to Rings can't achieve the goal because this tool is only used to measure the distance between two rings. But you can do it with pseudoatom.

Detailed procedure#

Preprocess#

1. Color the model with grey and followed with color it by element to see clearly.
2. Select the ligand and rename the object to 'ligand', then color it with magentas(or color you like).
3. Select the interactive residues: select the ligand, actions->around->residues with..., rename the object to 'active', then show the residues with sticks by show->side chain->sticks.
4. Hide valence with hide->valence, remove the hydrogen with remove hydrogen.
5. Find Polar Contacts: select the ligand, action->find->polar contacts->to others excluding solvent

Demonstrate pi-cation interaction#

1. Create pseudoatoms

   1. Switch the selecting mode to 'Atoms', click the atoms of the rings which need to generate a center one by one, the selected object is sele
   2. Run pseudoatom $NameOftheCenter, sele in command line.

2. Meausure the distance: wizard->measurement

3. Hide the pseudoatoms: hide->everything

Discussion#

1. Pi-cation interaction distance should be less than 6.6 angstrom, and pi-pi interactions are generally represented by green.
2. Pi-pi interaction distance should be less than 7 angstrom【2】, and pi-pi interactions are generally represented by blue.

reference:#

1. https://www.bilibili.com/video/BV1ZK4y1j7AW/
2. Shao, Jinfeng. / Evaluation of π-π interactions in proteins using Trp analogs : From protein labeling to quantitating the energies involved. [Groningen] : University of Groningen, 2016. 127 p.

此文由 Mix Space 同步更新至 xLog
原始链接为 https://xxu.do/posts/academic/Demonstrate-pi-pi-and-pi-cation-interaction-with-pseudoatom-in-pymol