[Chimera-users] assigning secondary structure

[Elaine Meng]

Hi Puey,
Yes, there are many different ways to assign values of these residue  
attributes, named isHelix and isSheet (or isStrand).  Here are five  
possible ways:

(A) by editing/adding HELIX and SHEET records in the input PDB file
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
pdbintro.html#secondary

(B) by running ksdssp in Chimera if you want the Kabsch & Sander DSSP  
method to figure out the assignments using your preferred parameter  
values
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html

(C) by creating an attribute assignment file
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ 
defineattrib.html#attrfile
and reading it in with Define Attribute
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ 
defineattrib.html

(D) by using the command "setattr"
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html

For example:
   setattr r isHelix true :1-10.a,23-36.b
   setattr r isSheet false :1-10.a,23-36.b

(E) by selecting residues, opening the Selection Inspector (one way is  
to click the button on the lower right corner of the Chimera window),  
and changing the "Residue" attributes "in helix" and "in strand"

** Be careful to avoid making both of those attributes true for the  
same residue, because Chimera will allow it.  If a residue is first  
assigned as helix and you want it to be strand, you need to both set  
isHelix false and set isSheet true. **

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Apr 21, 2007, at 7:15 AM, Puey Ounjai wrote:

> Dear all;
>
> I am wondering can we manually assign secondary structure to each  
> residues in the PDB file in chimera?
>
> Thanks
> Puey
>
>
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