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@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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