On Nov 9, 2005, at 12:34 PM, cjamesgrant@earthlink.net wrote:

Does chimera have the capability of automatically connecting the elements of a protein to reveal its overall shape. I am trying to determine the amino acid sequence of the attached protein, but I am having a hard time visualizing how the elements are connected to each other. I am new to this program, so any help would be greatly appreciated.

Thank you,

C Grant <Sequence_A.pdb>

Hi there, There are a lot of problems with that PDB file! Chimera will automatically connect atoms, except that this file has TER between each atom, forcing it to not include any bonds. Additional problems are that each atom is given a different residue number. It looks like these are normal amino acid residues, but instead of their usual names, the residue name throughout the file is PPP. I edited the whole file to be residue number 1 and removed all the TER lines, which is technically still very incorrect, but now you can visually tell the sequence of the peptide. The edited file is attached. To be technically correct you would have to name and number the residues correctly (looks like there are 14 of them). ----- 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