Dear Sotirios Katsamakas, You didn't say how you added the 25 amino acids. If I were adding them in Chimera, I would: (1) first build a peptide of the 25 amino acids as a separate model, using Build Structure (under Tools... Structure Editing), Start Structure section, "peptide sequence" -- this lets you specify all the phi and psi angles before the peptide is created <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...> (2) join the original protein and the new peptide using Build Structure, Join Models section <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...> So one possibility is to delete the 25 amino acids from that structure and build them again in Chimera as described above. A second possibility is to rotate each phi and psi angle in your current structure, using either Build Structure, Adjust Torsions section, or the "rotation" command. However, I think that would be difficult, or at least quite tedious and labor-intensive. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 13, 2012, at 5:40 AM, Sotirios Katsamakas wrote:

Dear sir or madam, I am a recent user of the chimera software on Linux-Ubuntu (11.10) operating system and I confronted a dead end on the following issue. I reconstructed a missing side chain of 25 amino acids in a PDB file but I cant seem to find how to set the secondary structure and so on for these 25 residues. So they are stuck in a linear formation externaly from my protein. For your consideration I am attaching also the PDB file. Thank you in advance and looking forward in hearing from you regarding my problem.

Best Regards, Sotirios Katsamakas

<1HVY-reconstructed_pdbv3.pdb>