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 <roja.r...@gmail.com> 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, <thomas.hol...@schrodinger.com> > wrote: > Hi Roja, > > This could be useful for you: > 18 Nov 2017, NME and ACE capping from script > https://www.mail-archive.com/pymol-users@lists.sourceforge.net/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 <roja.r...@gmail.com> 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. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net