Re: [PyMOL] NME and ACE capping from script

[Thomas H. <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.