> -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of George M. Sheldrick > Sent: 04 July 2008 13:42 > To: Matthew BOWLER > Cc: [email protected] > Subject: Re: [ccp4bb] Refmac unrestrained refinement on ligands only
> Perhaps what we > really need are B-value dependent distance and other > restraints, so they > are tighter if the B-values are higher and vice versa. I'm not so sure about that. The geometry SU's are supposed to reflect possible variations which are in the main due to differences in the chemical environment: for the original CSD structures from which the restraints were derived the experimental errors (< 0.01) are typically less than the RMSD's (> 0.01). The protein B factors clearly have very little to do with differences due to chemical environment, or even with the experimental errors in the CSD structures. If anything, bonds involving atoms with large B, particularly where the atoms are not part of a large rigid group such as an aromatic ring (e.g. in an aliphatic side-chain), are more likely to suffer from libration effects, and if this cannot be corrected by adjusting the target bond lengths, the only alternative should be to *increase* the SU's in order to allow the expected greater deviations from the 'ideal' mean value. Note that the goal of refinement is to construct the model that maximises the likelihood of making the observations, which is not the same thing as making a geometrically correct model (since the model that best fits the observations will be time & lattice-averaged and so will not necessarily have chemically valid geometry). In practice this is all academic: it's practically impossible to estimate the required corrections with sufficient accuracy, unless you have ultra-high resolution data, in which case restraints become irrelevant anyway. -- 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
