Hi Sarah, The part inside the parentheses is the atom name, as read from the input file. I can tell because these are the standard atom names used in PDB files. However, I don't understand what where/what you are scrolling over or in which program (how you got those strings with parentheses in them) -- when I put the mouse over an atom in Chimera, I get information that does not contain any parentheses. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 17, 2009, at 9:01 PM, Sarah Himes wrote:
Hi,
My name is Sarah Himes. I'm a graduate student at the University of Maryland. I'm researching alkaline phosphatase for an advanced course. I'm using the file 1ALK in Chimera. I'm pretty familiar with Chimera but I had a question regarding the letter notation of amino acid atoms when you scroll over them.
Here are some examples:
His370 (NE2) Ser102 (CB) Ser102 (N) Asp327 (OD1) Asp327 (OD2) Glu322 (OE2)
My question is, what do the letters in parentheses mean, what do they correspond to? When these letters show up in Chimera, there are no parentheses.
I look forward to hearing from you shortly. Thank you for your time.
Sincerely, Sarah Himes shimes@umd.edu 240-285-1251