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

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

Awesome, thanks so much Jared for your usefull suggestions!

all the best

james

вт, 25 июн. 2019 г. в 22:00, Jared Sampson <jar...@co...>:
>
> Hi James - Glad you got it working.
>
> > chains_array = ["A", "B"]
>
> If you want a list of chains without having to hard-code them, try the `get_chains` command.
>
> ```
> chains_array = cmd.get_chains()
> ```
>
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
>
> Alternatively, if you want to remove all the chain IDs (which it appears you might), you don't need a list of chains at all, and can just do:
>
> ```
> alter all, chain=''
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On June 25, 2019 at 11:48:32 AM, James Starlight (jms...@gm...) wrote:
>
> I have got it, it works now!
> in my example the double quotes were not escaped in pymol script :-)
>
> the only (more python-oriented) question, would it be possible to
> indicate chains_array for all letters A-Z (e.g. using some python
> regex, rather just for A and B, chains_array = ["A", "B"], like in my
> example?
>
>
> вт, 25 июн. 2019 г. в 17:22, James Starlight <jms...@gm...>:
> >
> > I actually tried to do like that still defining chains_array = ["A",
> > "B"] inside of pymol script and use external bash loop to loop over
> > pdbs
> > but it does not works ;(
> >
> > #!/bin/bash
> > # this script rename chains in pdb to "empty" chain
> > home=$(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 <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.
> > > >
>
>
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