Hi Pu Qian, I didn't know anything about Pymol's "alter," but from looking online it appears to have very broad functions. If you mean you just want to choose some residues and manually assign them as helix, for example, you can do that with the command "setattr," for example: setattr r isHelix true :10-15.A setattr r isStrand false :10-15.A Or, the more graphical way is to select the residues of interest, click the green magnifying glass on the bottom right corner of the Chimera window to show the Selection Inspector, inspect "Residue" and then change the "in helix" and "in strand" values. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 7, 2014, at 9:08 AM, Pu Qian <p.qian@sheffield.ac.uk> wrote:

Hi there, Sometime, when I use chimera to make a ribbon presentation of protein, the helix region will either broken or does not present properly. Similar thing can be happened in Pymol. But, Pymol provides a command called "alter". When I rebuilt it after altering, broken helix can be repaired. I'm wondering is there similar function in Chimera, or is there a suitable method which can be used to deal with it. Thanks Best regards Pu Qian