[Chimera-users] setting secondary structure of amino acid residues

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 28 15:36:54 PST 2014

Hi Haresh,
To run ksdssp, just enter command "ksdssp" … this does not change the coordinates of the structure, it just tries to identify which parts are helix and which are strand based on where it sees backbone H-bonds. If the ribbon is still not like the helix or strand width after you use "ksdssp" it means that the conformation does not look like helix or strand according to ksdssp.  

When you use addaa, make sure to specify the desired conformation.

Another way instead of addaa to build the 14 residues is with Build Structure (in menu under Tools… Structure Editing), section Start Structure, choice "peptide", which will then give a further dialog for setting phi/psi angles with suggestions available for different secondary structures.
You would build the peptide as a separate new model, but then use the Join Models section of Build Structure to attach it to the N-term of your protein.

HOWEVER, even if you built the conformation correctly, it depends whether you tried to make a strand or a helix.  Even if the peptide is in a beta-strand conformation, ksdssp will not identify a single strand by itself.  It only identifies a beta-strand when the backbone is positioned to H-bond with another beta-strand, as in a hairpin or sheet.

You could just force Chimera to show the residues as helix or strand no matter what the reality is or what ksdssp thinks, for example, selecting all those residues and then if you wanted them to be considered strand, using commands:
setattr r isHelix false sel
setattr r isStrand true sel
(just trade "isHelix" and "isStrand" in those commands if you wanted the residues to be considered helix)

For helix, an additional possibility is to try using ksdssp again but with command-line options to use less strict parameter values.  <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

You can search the manual for strings like "ksdssp" or "building peptides" from the Chimera Help menu.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 28, 2014, at 2:43 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:

> Hi Elaine,
> Yes I did exactly the way you explained and it is working now. 
> I have another question. I need to add some 14 residues on N-termius of the protein which I did using the addaa command. However, I am unable to simulate its secondary structure using ksdssp. I am not sure how to run this command in command line. Or am I doing something wrong in terms of predicting the structures.
> Can you please let me know what do I need to do in terms of getting the structure of protein after addsing residues on N-terminus.
> Thanks,
> Haresh

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