If you want to be 'by the book' on it, you should follow IUPAC rules for atomic numbering of chemical compounds. Unless you're an organic chemist, these rules are pretty hard to follow, so most people number at will.
If you're dealing with a 'known' series of compounds, such as analogous inhibitors developed in the course of a research project (say, in pharma industry) then typically you will see people refer to specific locations by number, and try to keep numbering consistent. Artem _____ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Zheng Zhou Sent: Monday, October 08, 2007 9:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to number atoms in a ligand Hi, all I am a rookie in crystallography. I know this may be a little bit off topic. I have cocrystallized several compounds with my favorite protein. I found crystal structures for some of these chemicals. But the numbering systems are different in those original papers for the small molecules. Some numbering system has all the atoms from 1 to the end (C1-O3-O8-N9-C15), while others have numbers for each individual element. (C1-C12, O1-O2, N1). I was trying to search a unified theme for ligands in pdb. I even emailed [EMAIL PROTECTED], but so far I haven't heard anything back. Could anyone give me some suggestions? Any help would be greatly appreciated. Thanks, Sorry to bother others Joe
