Re: [PyMOL] NME and ACE capping from script

Hi Thomas,

Thanks for your help! But the NME and ACE are added unattached and randomly
in the pdb. I simplified with a dipeptide AA instead. The file is attached
here.

Regards,
Simon

2017-11-18 17:04 GMT+08:00 Thomas Holder <tho...@sc...>:

> Hi Simon,
>
> I think this is the code you're looking for:
>
> from pymol import cmd, editor
> cmd.set('retain_order', 0)
> cmd.fab('APAPAPAP')
> editor.attach_amino_acid("last name C", 'nme')
> editor.attach_amino_acid("first name N", 'ace')
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> > On Nov 17, 2017, at 8:26 AM, Simon Kit Sang Chu <sim...@gm...>
> wrote:
> >
> > Hi everyone,
> >
> > I am generating segments of peptide to be used in GROMACS. I might be
> using amber which does not allow automatic capping. Therefore, I hope to
> solve it with Pymol.
> >
> > Currently, I use a pml scipt to generate the pdb file automatically. The
> script is simple.
> >
> > for aa in "APAPAPAP" : cmd._alt(string.lower(aa))
> > cmd.save("peptide.pdb")
> >
> > However, if I want to add NME and ACE caps, is there any residue code
> available? Like XAPAPAPAPY where X and Y are NME and ACE? The main point is
> to automize the process since I don't want to write NME / ACE manually
> everytime.
> >
> > I appreciate any suggestion and comment.
> >
> > Regards,
> > Simon
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>