Re: [PyMOL] PDB post-processing and TER records

[Thomas H. <tho...@sc...>]

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 <jms...@gm...> 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.