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> As IT said before, a reasonable distance cutoff seems > feasible. Perhaps 95% of all cases could be distinctly distinguished. I claim no credit for that idea! Refmac already uses a distance threshold to recognise chain breaks. > > The TER record might seem as a means to indicate gaps in the file, > but that leads to another problem: some check programs > (haven't deposited > lately, maybe PDB can comment) complain if OXT is missing at the > terminal record. However, putting an OXT on a chain that > continues and requires a N+1, is wrong. This decision requires a > cross-check against sequence. Still, it is doable. This shouldn't be a problem because you would never deposit with the intra-chain TER records present, they would all be removed prior to checking/deposition. They are only needed in the early stages of refinement (e.g. just after you've done a rigid-body refinement of individual domains), when using a distance threshold alone may give an incorrect indication of chain breakage. I would trust and hope that structures are never deposited in such a state! To be on the safe side in that situation you would probably want to flag _all_ chains breaks with TER records, regardless of distance. For a fully refined structure, a distance check (say 2 Ang.? - I've no idea what value Refmac uses) should be completely reliable in all cases because it's not likely that you would be depositing with any bonded C(i)-N(i+1) distances > 2 Ang., or any non-bonded ones < 2 Ang.! The biggest (and sadly I suspect insuperable!) problem is to get authors of model building & refinement programs to implement this usage of TER records (and of course to abandon usage of the residue number as an indicator of residue connectivity)! -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
