Just giving this thread a title. James
On May 3, 2011, at 10:06 AM, Ian Tickle wrote: > James, interesting that you chose residue number 32 for your example, > because that is the number of one of the two active-site ASPs in the > aspartic proteinase family (the other is ASP 215) that I (with Tom > Blundell & others) worked on for many years. So Ed, it's not just > relevant to the "Wu&Kabat numbering for antibodies". The idea that > one would _not_ use consistent numbering (and therefore insertion > codes) across species (viral, fungal, plant and animal so there is > huge sequence variability with insertions & deletions everywhere), > when working with these structures is frankly ludicrous. I recall > some programs (FRODO was one) actually required renumbering to the > ordinals, i.e. 1, 2, 3 ... - that is until I fixed it! This caused > endless confusion, not least because there are often other ASPs in the > vicinity of the active site which could easily get renumbered to 32. > For me, it's important that when I refer to 'ASP 32' there's no > possibility that I mean anything other than the active site ASP! > > Cheers > > -- Ian > > On Tue, May 3, 2011 at 5:17 PM, James Holton <jmhol...@lbl.gov> wrote: >> >> My understanding is that it was introduced for cases where an error in the >> sequence was discovered long after a large body of literature had >> accumulated for the "wrong" sequence. That is, imagine some enzyme where an >> important catalytic active site residue was number "152", and lots of people >> had been talking about this residue for years. Then, when you solve the 3D >> structure, you discover that there is actually a glycine between residues >> "32" and "33", what do you do? Do you change 152 to 153 and put up with all >> the angry letters from enzymologists, telling you that you mislabeled this >> important residue? In case you don't want to do this, the PDB allows you to >> put in a residue "32A". Deletions can happen too, but they are easier to >> deal with from a file format standpoint. >> >> -James Holton >> MAD Scientist >> >> On 5/3/2011 6:27 AM, Jahan Alikhajeh wrote: >> >> Dear Friends, >> I have noticed an issue in a pdb file, the term "insertion code". >> Does anyone know anything about it? what is it used for? >> Thanks in Advance, >> >> >> Jahan Alikhajeh, Ph.D, >> >> Technical Supervisor, >> >> MAN Corporation LTD, >> >> Keshavarz Boulevard, >> >> Ghods Avenue No. 41, >> >> 5th Floor, Tehran, Iran, 14177, >> >> Tel: +982166282841 >> >> Fax: +982166282997 >> >>
