CODEWITHSUNDEEP
pymol
Zubo
Zubo

Reputation: 1593

PyMol: select residues for which I have found hydrogen bonds

Using PyMol, I can show hydrogen bonds using Action -> Find -> Polar Contacts. This produces the contacts, but I want to show them clearly by only showing residues which have these contacts and nothing else (currently, the view is very unclear due to the rest of the protein ).

I want to select all residues that have the hydrogen bonds that I found. How can I do that?

Alternatively, what is a good way to show hydrogen bonds between two chains in a pocket, so that they are clearly visible?

Upvotes: 2

Views: 9008

Answers (1)

bunher
bunher

Reputation: 121

You can find contacts around a ligand or a part of a molecule by defining those contacts as a new selection. Please read about selections here (https://pymolwiki.org/index.php/Select) or select with the mouse and then go to (sele) and rename it. Use the name myligand. Then, in the command line, you can search for contacts in 3.5 Å distance and name this selection contacts:

select contacts, myligand around 3.5

Note that I chose 3.5 Å assuming you have a PDB file where hydrogen atoms are not mapped due to low resolution. Of course, you will get all contacts in this distance and not just hydrogen bonds, therefore you'd create a selection within myligand before that only contain your atoms that would potentially participate in H-bonds.

In the next step you create a new selection contactsfull containing the whole residues of contacts using byres:

select contactsfull, byres contacts

Now you can independetly style contactsfull and your protein. To display the H-bonds, I would then use Find -> Polar Contacts, wich creates another selection with only the H-bonds that you can style as you like.

Upvotes: 3

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