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

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

> 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 <jms...@gm...> 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 <jms...@gm...>:
>> 
>> 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 <tho...@sc...>:
>>> 
>>> 
>>>> On Jun 25, 2019, at 11:48 AM, James Starlight <jms...@gm...> 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.