Hi, I think you'll find that if you work out the contribution from f' to the density, in most cases it's not significant relative to the RMSD. This will be particularly true for S which of course has a low value of f' for all commonly used wavelengths. This must be true otherwise we would observe these effects routinely. The explanation must involve some effect which is peculiar to the crystal being studied, as opposed to being peculiar to the wavelength, and radiation damage seems the most likely explanation (and has been unequivocally demonstrated in a number of cases).
-- Ian > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Lijun Liu > Sent: 05 May 2008 21:37 > To: James Holton > Cc: [email protected] > Subject: Re: [ccp4bb] Negative density around C of COO- > > I believe some, may not be all, negative density may be due > to the choice of wavelength. C,O and N are not so sensitive > to normally used wavelength (1-1.54A), but S does. This is > more true when you have higher resolution and better quality > data. You can estimate this by f'. > > By the way, although I am not a real supporter of "radicals > from damage", I believe that a photo-induced (here X-ray) > chemical reaction is much different from a heat-induced one. > Low temperature is not a problem. But this not for > diffusion, as it is ~100% heat-related. Please point out if > I am wrong. > > This "assignment" of free radicals to damage is often > made (flippantly) in the literature, but I feel a strong need > to point out that there is NO EVIDENCE of a free radical > diffusion mechanism for radiation damage below ~130K. > > > Lijun Liu, PhD > Institute of Molecular Biology > HHMI & Department of Physics > University of Oregon > Eugene, OR 97403 > 541-346-4080 > > > 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
