> Interesting that the IUCr committee report that Ian pointed > out stated > "we recommend that the use of B be discouraged". Hmm... Good > luck with > that!
You seem to be implying, if I understand you correctly, that the IUCr report recommends that the use of the equivalent isotropic B be discouraged, but that's not what it says! The recommendation concerning B comes in section 2.1 "Anisotropic displacement parameters", just after eqn. 2.1.27. But in fact it's clear from that equation, where B is a tensor, that it's talking about the *anisotropic* B tensor. In the following main section 2.2 "Equivalent isotropic displacement parameters" no such recommendation appears. Also in section 4 at the end where the recommendations are summarised it explicitly says (point 7) "Avoid using the Gaussian anisotropic parameters that are now usually symbolized as B^ij and are defined in eq. (2.1.26). These quantities are directly proportional to the recommended U^ij , the ratio being 8pi^2". Again, no mention of a recommendation concerning the equivalent isotropic B. Indeed of course, the PDB follows the IUCr recommendations (actually it was more a case that the IUCr accepted the de facto existence of the PDB!), i.e. equivalent isotropic B's and anisotropic U's. B^ij's are indeed used internally by some software for convenience in intermediate calculations, but since the output values are U's there's no problem with that. This raises a point relevant to your original suggestion concerning a new name for the unit of B: in a PDB file the U^ij values are actually 10000*U^ij, in order to save space by eliminating non-significant digits, as I pointed out previously. However, does this mean that one should think of the values in the file as being in units of picometres^2 (it took me a few moments to work that out!), or does it mean that the values are to be thought of as 10000*U^ij so that the units are still the familiar A^2? So by analogy values of B are to be thought of as 8pi^2*U (that's what the equation B = 8pi^2*U means after all!), but still in units of A^2. I suspect that most people, like me, would think of it in those terms. Cheers -- Ian > I agree that I should have used "U" instead of u^2 in my > original post. > Actually, the "u" should have a subscript "x" to denote that > it is along > the direction perpendicular to the Bragg plane. Movement within the > plane does not change the spot intensity, and it also does > not matter if > the "x" displacements are "instantaneous", dynamic or static, > as there > is no way to tell the difference with x-ray diffraction. It just > matters how far the atoms are from their ideal lattice points (James > 1962, Ch 1). I am not sure how to do a symbol with both superscripts > and subscripts AND inside brackets <> that is legible in all email > clients. Here is a try: B = 8*pi*<u<sub>x</sub>^2>. Did that work? 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 i.tic...@astex-therapeutics.com 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
