Hi Nurul, If the input protein PDB file has HELIX and SHEET information, that information is used. If the input file does not have secondary structure information, the "ksdssp" function is automatically used to assign it. This is an implementation of the DSSP method. More information: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html Again, you do not have to run it because it will be run automatically if the input file does not have secondary structure information. However, you can re-run the algorithm if you want to use different parameters. Here are a couple of ways: (1) use the "ksdssp" command (as described in the link above) or (2) in the Model Panel (Favorites... Model Panel), choose the models of interest on the left, change from "frequently used" functions to "infrequently used," and then click "compute SS" on the right. 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 Jan 10, 2007, at 12:12 AM, nurul wrote:

hello

i'm a student from malaysia and i'm using chimera in my studies, i have one question regarding this software, how does it assign the secondary structure? is it using dssp or stride or any other secondary structure assignment program? thank you _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users