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! вт, 25 июн. 2019 г. в 16:03, Thomas Holder <thomas.hol...@schrodinger.com>: > > > generally if I integrate a pymol silent script inside my > > bash script, I do not need to use cmd.* syntax, right? > > Correct. The -d argument takes PyMOL commands, like a .pml script. Python > syntax is optional. > > Python syntax (cmd.*) is necessary and most useful if you write a Python > script (.py extension) and run that with PyMOL. You could write your > multi-chains loop as a Python script: > > ################ example.py ########## > from pymol import cmd > pdb = "my.pdb" > chains_arrays = ["A", "B", "C", "D", "E", "F", "G"] > > for chain in chains_array: > cmd.load(pdb) > cmd.alter('chain ' + chain, 'chain=""') > cmd.save('output_' + chain + '.pdb') > cmd.delete('*') > ###################################### > > Then run it with PyMOL: > pymol -ckqr example.py > > See also: > https://pymolwiki.org/index.php/Launching_From_a_Script > https://pymolwiki.org/index.php/Python_Integration > > Cheers, > Thomas > > > On Jun 25, 2019, at 3:08 PM, James Starlight <jmsstarli...@gmail.com> wrote: > > > > one extra programming question: > > > > imagine now in my pdb I have severals chain which I would like to > > rename to blank chain. > > > > I can do it simply like this > > # a case for 3 chains to be renamed > > > > #!/bin/bash > > pdb="my.pdb" > > output=$(pwd) > > pymol -c -d " > > cmd.load('${pdb}') > > cmd.alter('(chain A)', 'chain=\"\"') > > cmd.alter('(chain B)', 'chain=\"\"') > > cmd.alter('(chain C)', 'chain=\"\"') > > cmd.save('${output}/output.pdb','all') > > " > > > > or for multi-chain protein I can alternatively create external loop, > > thus running pymol 3 times iteratively (which is not good realization) > > providin array info from external shell session > > > > # this example save 7 different pdbs renaming one chain in each of them > > #!/bin/bash > > pdb="my.pdb" > > output=$(pwd) > > chains_arrays=( A B C D E F G ) > > > > for i in "$chains_array[@]}"; do > > pymol -c -d " > > cmd.load('${pdb}') > > cmd.alter('(chain $i)', 'chain=\"\"') > > cmd.save('${output}/output_$i.pdb','all') > > " > > done > > > > would it be possible rather to make an array and loop inside the pymol > > to rename all chains into the blank chain during one execution of > > pymol? > > > > Thanks in advance! > > > > вт, 25 июн. 2019 г. в 14:50, James Starlight <jmsstarli...@gmail.com>: > >> > >> I have got the idea! > >> thank you so much Thomas! > >> One question: generally if I integrate a pymol silent script inside my > >> bash script, I do not need to use cmd.* syntax, right? In what cases > >> cmd.* sytax might be usefull? > >> > >> Thank you again! > >> > >> вт, 25 июн. 2019 г. в 12:05, Thomas Holder <thomas.hol...@schrodinger.com>: > >>> > >>> > >>>> On Jun 25, 2019, at 11:48 AM, James Starlight <jmsstarli...@gmail.com> > >>>> wrote: > >>>> > >>>> so what I need is just to update my pymol, keep using the same command? > >>> > >>> Yes > >>> > >>>> P.S.would the following integration of the code into bash script be > >>>> usefull to remove chains in no gui mode? > >>>> > >>>> pymol -cQkd " > >>>> from pymol import cmd > >>>> fetch $pdb, type=pdb, tmp > >>>> cmd.alter('(chain A)',chain='') > >>>> " > >>>> I am not sure whether I used here cmd.alter in correct way .. > >>> > >>> > >>> With fetch, use "async=0" or use Python syntax. And keyword arguments > >>> (type=) must be after positional arguments (tmp). > >>> > >>> It's easier if you don't use Python syntax for alter, otherwise you'll > >>> need three levels of nested quotes, which gets ugly: > >>> > >>> pymol -cQkd " > >>> fetch $pdb, tmp, type=pdb, async=0 > >>> alter (chain A), chain='' > >>> " > >>> > >>> With Python syntax (note the ugly escaping of quotes): > >>> > >>> pymol -cQkd " > >>> cmd.fetch('$pdb', 'tmp', type='pdb') > >>> cmd.alter('(chain A)', 'chain=\"\"') > >>> " > >>> > >>> Cheers, > >>> Thomas > >>> > >>> -- > >>> Thomas Holder > >>> PyMOL Principal Developer > >>> Schrödinger, Inc. > >>> > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe