Hello Friends,
I have a question about pymol an I was wondering if you could advise me.
How can see salt bridges of a protein in Pymol?!
Try by identifying polar contacts (built-in PyMOL function) between charged side chains. Otherwise, have a look through https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/ , that is what I used earlier
Select salt bridge contacting groups, after that selected section's [A] Action -> Find -> Polar Contact -> Within selection.
In PyMOL, if you want just the salt bridges between protein side chains, you can define two selections:
select negative, (resn ASP+Glu and name OD*+OE*)
select positive, (resn Lys and name NZ) or (resn arg and name NE+NH*)
You might want to also add in the terminal charges: for each chain,
select negative, negative or (name OXT or last ([your chain] and name O))
select positive, positive or first ([your chain] and name N)
If you have other charged groups, either postranslational modifications or cofactors you want to include, you have to alter the two selections accordingly
Once you have defined the groups of positively and negatively charged atoms, you can identify the salt bridges between the two dependent on the distance cut-off
distance saltbridge, negative, positive, 4.0, 0
This could be best option
https://projects.biotec.tu-dresden.de/plip-web/plip/index
I would have suggested PLIP too. However, the webserver only analyzes contacts between Proteins and small molecules. To analyze Protein-protein interactions, you have to download and install PLIP locally, then run it over the commansline.
Hello!
I have 7 proteins. One central which is surrounded by others. I wanna determine negative and positive residues on central protein and surrounds separately. What command do you recommend?
If you just want to represent a subset of the salt bridges in your object, you can modify the selection. Assuming you want to only show the salt bridges between chain A in structure and the other chains in your structure: you define the negative and positive charged atoms as described earlier:
select negative, (resn ASP+Glu and name OD*+OE*)
select positive, (resn Lys and name NZ) or (resn arg and name NE+NH*)
now you can define the interchain salt bridges as:
distance saltbridge1, (negative and chain A), (positive and not chain A), 4.0, 0
distance saltbridge2, (positive and chain A), (negative and not chain A), 4.0, 0
Note that you have now to distinguish between salt bridges in which the negative charge is in chain A and those there the positive charge is in chain A.
If the seven proteins are not chains within the same object, but separate objects, you have to modify the selection accordingly:
distance saltbridge1, (negative and object1), (positive and not object1), 4.0, 0
distance saltbridge2, (positive and object1), (negative and not object1), 4.0, 0
Have a look at https://pymolwiki.org/index.php/Property_Selectors, https://pymolwiki.org/index.php/Selection_Algebra, https://pymolwiki.org/index.php/Single-word_Selectors, https://pymolwiki.org/index.php/Selection_Macros
to learn about working with selections in PyMOL. You might also want to have a look at this: Intermediate PyMOL
Thank you so much!
To be honest, I looked at intermedate pymol but I didn't get much. Now that I am having your explanaition I will look at it again to understand better.
Best,
This tutorial might be helpful
https://www.google.si/url?sa=t&source=web&rct=j&url=https://m.youtube.com/watch%3Fv%3Duxa-9UYnIAw&ved=0ahUKEwiDvP3qzNfbAhVIthQKHZyGDboQwqsBCDMwAg&usg=AOvVaw0ybr0i5gr4o9r5pYrqzw1c
Regards
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