Hi Eugene > If I were to deal with your example, I would look into distance > profile between residues in coordinate section, which then > gives answer to your question.
OK that's interesting, I hadn't realised that the interatomic distances played an active role in determining connectivity: I had assumed the whole point of the various connectivity specifiers was to avoid reliance on distance calculations. But resolution of the kind of ambiguity I illustrated would not occur automatically, or would it? - i.e. would the need for it only become clear when the structure was checked manually? Of course it makes sense to use distance information for fully-refined structures such as those that are (hopefully!) deposited with the PDB, but it would be more of an issue with refinement programs that have to deal with all kinds of errant input geometry! I suppose the fundamental problem is that we're trying to use the same format for both purposes and there are fundamentally conflicting requirements. Cheers -- 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. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
