I actually tried to do like that still defining chains_array = ["A",
"B"] inside of pymol script and use external bash loop to loop over
pdbs
but it does not works ;(
#!/bin/bash
# this script rename chains in pdb to "empty" chain
home=$(pwd)
pdb_folder=$home/pdbs
output=$home/output
rm -r $output
mkdir $output
#pymol -cQkd "
for pdb in "${pdb_folder}"/*.pdb ; do
pdb_name2=$(basename "${pdb}")
pdb_name="${pdb_name2/pdb}"
pymol -c -d "
from pymol import cmd
chains_array = ["A", "B"]
cmd.load('${pdb}')
cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
" > $output/pymol_${pdb_name}.log
done
вт, 25 июн. 2019 г. в 16:58, James Starlight <jmsstarli...@gmail.com>:
>
> 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 <thomas.hol...@schrodinger.com>:
> >
> > 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 <jmsstarli...@gmail.com>
> > > 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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