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

[James S. <jms...@gm...>]

yes, actually it is better because we avoid looping!
and how it would be possible to use array provided in the externall shell?

#!/bin/bash
pdb="final.pdb"
output=$(pwd)

# array given in bash
chains_array=('A' 'B')

# chains are cutted by pymol
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('output_without'+"".join($chains_array) + '.pdb')
"

вт, 25 июн. 2019 г. в 16:47, Thomas Holder <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.
>