Insertion codes are a commonly used part of the PDB specification. It's odd that they wouldn't be supported correctly. To take another similar case, what would you say of a program that couldn't handle negative residue numbers as is commonly done with N-terminal purification tags? "All sequences must start with 1"? (Not all antibodies are isolated from natural sources. Some are from human-designed libraries for example, so they are every bit as engineered as something with as His tag stuck on the end.)
Cheers, Eric On Jun 16, 2014, at 7:23 AM, Ed Pozharski wrote: > There is no actual requirement to use Kabat numbering, you can avoid it > alrogether. Some argue that L27A is actually 28th amino acid in the protein > sequence, and labeling it as L27A is simply incorrect. I would suggest doing > refinement with plain numbering (no insertion codes) and changing it only for > the final model if needed for comparative analysis. > > Ed > > > Sent on a Sprint Samsung Galaxy S® III > > > -------- Original message -------- > From: "Hargreaves, David" > Date:06/16/2014 6:07 AM (GMT-05:00) > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Kabat, insertion codes & refinement > > > Dear CCP4bb, > > > > I’m refining an antibody structure which requires Kabat residue numbering > with insertion codes. My setup of Refmac5 and Buster both break peptide bonds > between some (not all) of the residues with insertion codes. I was wondering > whether there is a special way of handling these residues in refinement? > > > > Thanks, > > > > David > > > > David Hargreaves > > Associate Principal Scientist > > _____________________________________________________________________ > > AstraZeneca > > Discovery Sciences, Structure & Biophysics > > Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF > > Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 > > David.Hargreaves @astrazeneca.com > > > > Please consider the environment before printing this e-mail > > > > > > > AstraZeneca UK Limited is a company incorporated in England and Wales with > registered number: 03674842 and a registered office at 2 Kingdom Street, > London, W2 6BD. > > > Confidentiality Notice: This message is private and may contain confidential, > proprietary and legally privileged information. If you have received this > message in error, please notify us and remove it from your system and note > that you must not copy, distribute or take any action in reliance on it. Any > unauthorised use or disclosure of the contents of this message is not > permitted and may be unlawful. > > > Disclaimer: Email messages may be subject to delays, interception, > non-delivery and unauthorised alterations. Therefore, information expressed > in this message is not given or endorsed by AstraZeneca UK Limited unless > otherwise notified by an authorised representative independent of this > message. No contractual relationship is created by this message by any person > unless specifically indicated by agreement in writing other than email. > > > Monitoring: AstraZeneca UK Limited may monitor email traffic data and content > for the purposes of the prevention and detection of crime, ensuring the > security of our computer systems and checking compliance with our Code of > Conduct and policies. > > > > > > > > > > > > > > -- Eric Bennett, er...@pobox.com Always try to associate yourself with and learn as much as you can from those who know more than you do, who do better than you, who see more clearly than you. - Dwight Eisenhower
