Sorry if the original got through, but my server keeps telling me it was unable to send this, so I've sent it again. My apologies if it was originally delivered
-Haydyn -------- Original Message -------- Subject: rhombicity confusion Date: Fri, 25 Apr 2003 14:44:15 +1000 From: haydyn mertens <[email protected]> To: [email protected] Hi guys, I'm currently implementing RDCs into my NMR structure calculations for a small protein domain. The confusion I've stumbled into surrounds the definition of rhombicity. Q. When is the rhombicity in the range 0 - 1? Q. When is the rhombicity in the range 0 - 2/3? I'm making the assumption that estimations of axial and rhombic terms from a powder-pattern distribution (histogram) yield the rhombicity "R", as defined by Clore et al., with a max. R of 2/3. My data yields a value of ~0.6 when obtained by this method. However, when applying the maximum-likelihood method (Warren & Moore, JMR, 149, 271-275 (2201)) I obtain "most-likely" R values of 0.74 +- 0.03 . I have also successfully run the ISAC method (Sass et al., JBNMR, 21, 275-280, 2001) yielding a rhombicity of 0.77 +- 0.02 . In this case it is my understanding that the max. R is 1, due to the definition of rhombicity as: R=(Axx - Ayy)/Azz , and the equation for dipolar coupling used: D=Azz/2*[(3cos2(theta) -1) + R*(sin2(theta)cos2(phi)) So in this case I would multiply this value of R by 2/3 to use it in a SANI run in CNS. I think? In XPLOR-NIH and CNS the equation for dipolar coupling used is: D=Da*[(3cos2(theta) -1) + 3/2*R*(sin2(theta)cos2(phi))] with R=Dr/Da, and Da=1/3*(Dzz-(Dxx+Dyy)/2), Dr=1/3*(Dxx-Dyy). Using Dxx+Dyy+Dzz=0, the rhombicity R is: R= 2/3*(Dxx-Dyy)/Dzz , with a max. value of R=2/3 So, is R always (Dxx-Dyy)/Dzz ? and when quoted as "R" always between 0 and 1? Or is R sometimes quoted as "R" with the author meaning R=2/3*(Dxx-Dyy)/Dzz ? If any of you guys can set me straight on this I'd really appreciate it, as I'm spending a lot of time trying to figure this out. In particular, if anyone has used the maximum liklihood method to estimate the value of R I'd love to know whether values greater than 0.66 are reasonable. Thanks in advance, Haydyn -- ------------------------------------------- Haydyn Mertens PhD student Department of Biochemistry University of Melbourne Australia
