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 <[email protected]> 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, <[email protected]>
> wrote:
> Hi Roja,
>
> This could be useful for you:
> 18 Nov 2017, NME and ACE capping from script
> https://www.mail-archive.com/[email protected]/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 <[email protected]> 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.
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