Re: [PyMOL] Capping of multiple pdb file using python script in pymol

[shivani s. <shi...@gm...>]

Hi Thomas,

Thanks for your reply. I am currently using:
















*import __main____main__.pymol_argv = ['pymol','-qc']from pymol import cmd,
editorpymol.finish_launching()import globimport ospath =
os.path.dirname(pymol.__script__)pdb_files = glob.glob(os.path.join(path,
'*.pdb'))cmd.delete('all')for pdb in pdb_files:    cmd.load(pdb)
editor.attach_amino_acid("resi 10 and name N", 'ace')
editor.attach_amino_acid("resi 11 and name C", 'nme')    cmd.save(pdb)
cmd.delete('all')*

This seems to be working fine for me.

Shivani

On Thu, 14 Oct 2021 at 00:22, Thomas Holder <th...@th...> wrote:

> 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 <shi...@gm...> 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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