[Chimera-users] chimera utility help

[Elaine Meng]

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.html#start>

(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.html#join>

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.html#adjust>
<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>