Hi Shivani,
Your selection needs to be object-specific, e.g. like this:
for filename in glob("*.pdb"):
cmd.load(filename)
obj = filename[:-4]
editor.attach_amino_acid(obj + " and resi 10 and name N", 'ace')
Hope that helps.
Cheers,
Thomas
> On Oct 9, 2021, at 21:18, shivani sharma <[email protected]> wrote:
>
> Hi everyone,
>
> I am trying to cap (with ace and nme) various *.pdbs. I made a folder, where
> I have placed *.py file and *.pdb files. When I load the run following script:
>
> from pymol import cmd, editor
> from glob import glob
> for filename in glob("*.pdb"):
> cmd.load(filename)
> editor.attach_amino_acid("resi 10 and name N", 'ace')
> editor.attach_amino_acid("resi 11 and name C", 'nme')
>
> It is opening all files but capping only one of the files and giving me back
> an error:
> Traceback (most recent call last):
> File "pyformol.py", line 6, in <module>
> editor.attach_amino_acid("resi 10 and name N", 'ace')
> File
> "C:\Users\Shivani\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pymol\editor.py",
> line 129, in attach_amino_acid
> raise pymol.CmdException("invalid connection point: must be one atom, name
> N or C.")
> pymol.CmdException: Error: invalid connection point: must be one atom, name
> N or C.
>
> This seems like a looping error. I haven't been able to find much about
> "glob". Could someone suggest an easy way out? I want to create a loop where
> ace and nme should be added to all the dipeptides and save them as separate
> pdb files.
>
> Shivani
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