For those of us who are command-handicapped such as me: On the bottom right you can change the range of your selection (atoms, residues, chains... ) pick whatever is best for you and then click on the structure the appropriate atoms, then right-click and your will see a pop-up menu where you can "remove" the selected atoms/residues/whatever.

You can also display the sequences click on the S on the bottom right, and then directly select the residues you want to delete, then right click...

Dear Mr. kaushal,

First you must select particular atoms in a residue and named it using select command.For example ca (alpha carbon and N in residue number 100) :

PyMOL> select alpha_c_n, resi 100 and name ca+n

then remove selection using :

PyMOL> remove alpha_c_n

in other hand you can use this command directly:

PyMOL> remove resi 100 and name ca+n

Hope it helps,

HHA

For those of us who are command-handicapped such as me: On the bottom right you can change the range of your selection (atoms, residues, chains... ) pick whatever is best for you and then click on the structure the appropriate atoms, then right-click and your will see a pop-up menu where you can "remove" the selected atoms/residues/whatever.

You can also display the sequences click on the S on the bottom right, and then directly select the residues you want to delete, then right click...

Thank you so much Mr. M. Eugenio Vazquez for our kind response. I'll do it the same and if any problem let you know.

After removing the atoms in PyMol, is it possible to make the protein adjust itself and change its structure accordingly? Or does removing atoms in PyMol just mean that the space is empty in PyMol?

Hi Radhey,

     Import your .pdb file in pymol and go to Display----> Sequence.

    Then Drag the residues which you want to remove from the protein. Now Right Click the Dragged residues -----> click remove .

All the Best.

Priyanka, the protein does not adjust itself. PyMol only represents the atoms, but once edited, that's not a "real" structure anymore.