[Chimera-users] Manually assigning secondary structure to residues

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 16 09:10:41 PDT 2007

Hi Oren,
Yes, you can simply assign residues as helix or strand "manually."   
Here are a couple of ways:

(A) select the residue(s), open the Selection Inspector (by clicking  
the button on the bottom right corner of the Chimera window that says  
what is selected), switch to Inspect "Residue," and then set the "in  
helix" and "in strand" true/false attributes as desired.

There are many ways to select the residues in the first place: by  
picking from the screen, in the model's Sequence panel (under  
Tools... Structure Analysis), with a command ( example: select : 
12.a ), etc.

(B) use the command "setattr":

For example, the following would assign all currently non-helix non- 
strand residues as helix:
setattr r isHelix true :/!isHelix and !isStrand

I should note that the assignment is done by our implementation of  
Kabsch & Sander's DSSP, and the behavior reflects both the general  
methodology and the parameter settings.  You can change the parameter  
settings to be used when a structure is read (albeit not the method)  
in the "compute SS" dialog opened from the Model Panel (itself under  
Favorites).  I don't know if adjusting those parameters would  
eliminate the end effects you are seeing, however.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 16, 2007, at 3:23 AM, Oren Shalev (Wolfshtat) wrote:

> Dear Chimera team and users,
> I'm modeling chains with gaps using in-house software. When opening  
> in Chimera a model in which a secondary structure element is broken  
> or flanked by the start/end of a gap, the secondary structure of  
> the residue adjacent to the gap is assigned to be 'coil'. I guess  
> this is expected, since one needs to know both Phi and Psi angles  
> to determine the secondary structure of a given residue, yet I  
> always have knowledge that the residue adjacent to the gap does  
> indeed belong to a secondary structure element.
> My question is this: is there a way to assign the secondary  
> structure of a given residue to either 'helix' or 'strand'? I'm  
> interested in this for imaging purposes, so potential negative  
> consequences on other aspects of Chimera's operation (perhaps on  
> analysis tools?) don't matter to me.
> Thank you,
> Oren
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