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 <simoncks1...@gmail.com> > 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. ------------------------------------------------------------------------------ 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