If you want to rename multiple chains at once, make a selection like (chain
A+B+C). This list selection syntax is documented here:
https://pymolwiki.org/index.php/Property_Selectors
cmd.load(pdb)
cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
cmd.save('output.pdb')
Cheers,
Thomas
> On Jun 25, 2019, at 4:14 PM, James Starlight <[email protected]> wrote:
>
> thanks so much Thomas, for this example!
>
> Actually, your python script does exactly what my bash script -
> produces number of pdbs for each of the renamed chain.
> I would like rather to produce at the end ONE pdb with all chains
> renamed to empty chain...
> I guess I need to save the result outside of the loop something like this
>
> ################ hop hey lalaley #####
> from pymol import cmd
> pdb = "Ev_complex_model_final.pdb"
> chains_array = ["A", "B"] # add more chains in case of more complex pdb
>
> # loop over chains to rename it
> for chain in chains_array:
> cmd.load(pdb)
> cmd.alter('chain ' + chain, 'chain=""')
> cmd.delete('*')
> ######################################
>
> # save output as pdb
> # I need to add something in the name of output indicating how much
> chains have been renamed
> # like output_withoutAB.pdb
> cmd.save('output_' + '.pdb')
>
> thanks in advance for help!
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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