On Tuesday, February 1, 2005, at 12:14 AM, Jagannadh Dr B, Scientist wrote:

Hi, I am new to Chimera Can any one suggest how one can draw a ribbon for a peptide which has non-standard residues Jagannadh

Hi Jagannadh, If these nonstandard residues have the same backbone atoms as regular amino acids (N, CA, C, O), it might work already, although it depends on how these residues were specified in the input file. For example, many PDB files have the nonstandard residue selenomethionine, MSE, but the ribbon is drawn just like for the other residues (one such PDB file is 1kko). However, it sounds like you already tried and did not get a ribbon for these residues. It must be that the backbone is different or even that the backbone atoms have different names than N, CA, C, O. You can use the "Residue Class" section of Ribbon Style Editor (Tools... Graphics... Ribbon Style Editor) to define which atoms determine the path of the ribbon for these nonstandard residues. The instructions for creating a Residue Class can be viewed at: http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ ribbonstyle/ribbonstyle.html#class Then, you could select the nonstandard residues and then Apply the class you have created to those residues. I can't really get more specific without knowing more about these nonstandard residues, but you can send me e-mail if you get stuck. I hope this helps, Elaine ---- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html