Re: [PyMOL] selection of a set of amino acids

Hi Alireza - For renumbering a chain, the program PDBSET in the CCP4 suite is my tool of choice. If your protein is chain A, the command would look something like this: pdbset xyzin my_protein.pdb xyzout my_protein_renumbered.pdb

Re: [PyMOL] selection of a set of amino acids

Thanks for your prompt answer, numbers resets in every chain - and there is a lot of nucleobases in the beginning (A,C,U,G) and MG at the end and these atoms mess up the residues number additionally ! can I remove them via pymol ? Thank you On Sat, Dec 13

Re: [PyMOL] selection of a set of amino acids

Hi, There is a script available on the pymol wiki called "zero_residues". This will allow you to easily renumber any AA sequence. As far as other heteroatoms are concerned you could consider removing them (remove hetatm), or extract them into a second object. Another alternative is to simply adjus