Re: [ccp4bb] How to number atoms in a ligand
Dear Joe, Atom labels are, in principle, arbitrary. The molecule doesn't case what we call its atoms. To make the PDB more useful, it is handy if all the people working with a particular compound use the same names for their atoms. If you find that someone has already deposited a structure containing your compound you are expected to use the same names they did. There are lists of compounds and naming conventions on the PDB web site. The small molecule literature doesn't count as precedence for naming conventions, only what is in the PDB. No one will hold you to the names used in the small molecule structure paper. If you are the first to work with this compound in the macromolecular world you are free to choose whatever names you want. Please choose something sensible as the rest of use will be stuck with your choice forever. Consistency is king here. If a similar compound is in the PDB, using atom names based on it would simplify comparisons. Dale Tronrud Zheng Zhou wrote: 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] mailto:[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
Re: [ccp4bb] How to number atoms in a ligand
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
