How to edit a pdb file of a dimeric protein so that dimer can be converted and saved as monomer pdb which can be used in docking experiment.
You can open the pdb file in a plain text editor, e.g. Notepad+ on Windows, and copy/paste all ATOM/HETATM lines with the same chain label into a new file.
You can also open the pdb file in a molecular viewer program, e.g. PyMOL.
For example:
load 2XEE
this file contains 4 chains with chain labels A, B, C and D
create 2XEE_A, 2XEE and chain A
creates an additional object that just contains chain A
alternatively you can directly save chain A into a new pdb file with:
save 2XEE_A.pdb, /2XEE//A
Open the pdb file of the dimeric protein in pymol. See the sequence for chain information. Delete the sequence (chain/chains) such that only the sequence of the monomer remains. Save the file.
You can do it through Discovery studio... open the pdb file and delete the portion that you want to remove.
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