Re: [PyMOL] Add ACE and NME terminals

Hi Roja,

Which PyMOL version do you use? The "attach_amino_acid" function had a bug in old versions, it was fixed in PyMOL 1.8.0.

A capped poly-threonine alpha helix can be built in PyMOL (1.8+) like this:

from pymol import cmd, editor
cmd.set('retain_order', 0)
cmd.fab('T' * 40, ss=1)
editor.attach_amino_acid("last name C", 'nme')
editor.attach_amino_acid("first name N", 'ace')

Cheers,
  Thomas

> On May 10, 2018, at 8:53 AM, roja rahmani <roj...@gm...> wrote:
> 
> Dear Thomas,
> 
> I tried both builder and command. But the problem is an NME doesn't connect to last C, even when i remove the last OXT.
> 
> Let me ask in different way. Please help me to build poly threonine(consist of 40 threonine amino acids) in alpha helical structure which is capped by NME and ACE. How can i exactly build it?
> 
> (I want to use its .pdb file as an input for amber99ff in GROMACS.)
> 
> Best regards
> -Roja
> 
> On Thu, 10 May 2018, 00:47 Thomas Holder, <tho...@sc...> wrote:
> Hi Roja,
> 
> This could be useful for you:
> 18 Nov 2017, NME and ACE capping from script
> https://www.mail-archive.com/pym...@li.../msg14812.html
> 
> I couldn't quite follow your description, which interface were you using? The "Builder" panel? The following works for me:
> 1) Click "Builder" button in the upper right
> 2) Click "Protein" tab
> 3) Click "NMe"
> 4) Click on the last C atom (C-terminus)
> 
> If there is an OXT atom, remove that first (e.g. with: "remove name OXT")
> 
> Hope that helps.
> 
> Cheers,
>   Thomas
> 
> > On May 9, 2018, at 9:11 PM, roja rahmani <roj...@gm...> wrote:
> > 
> > Hi,
> > 
> > I'm beginner in PYMOL. I want to add ACE and NME terminals to helical poly amino acid which is made by Peptide builder. I load the poly AA pdb file to pymol. Then:
> > 
> > Edit first (name N) 
> > 
> > Then i didn't know how to add residue so i got help from taps and select ACE.
> > But when i used this command,
> > Edit last (name C)
> > And then select NME from tabs, the NME were not connected to the last carbon and was completely separated.
> > Would you please help me how solve this problem?
> > 
> > Best regards
> > Roja

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.