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": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html 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 ----- 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 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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users