Yep, agree completely! My point was that if you try to bypass the TLS parameters, then you still need to retain the anisotropic component somehow. But I wasn't advocating it.
I believe the simplest and most honest thing to deposit are the parameters of your model, viz the TLS parameters and the residual B factors. Derived quantities should be calculated as and when you need them. But I recognise there are genuine concerns about the lack of software support for new (?) model parameterisations. There is software for inter-converting but it is not always used, and you don't always know what you are starting with. m -----Original Message----- From: CCP4 bulletin board on behalf of Robbie Joosten Sent: Sat 3/29/2008 8:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rant: B vs TLS, anisou, and PDB headers ANISOU records imply that individual anisotropic B-factors were refined. This will cause problems when you try to redo the final refinement: you add loads of parameters all of a sudden. Using ANISOU records may give you more reliable information about the B-factors, but not about the refinement. Cheers, Robbie Joosten From: "Winn, MD (Martyn)" <[EMAIL PROTECTED]> Sent: Saturday, March 29, 2008 20:57 To: <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] [phenixbb] Rant: B vs TLS, anisou, and PDB headers >> 2) All you need to reproduce the R-factors are the ATOM records and >> structure factor formula (and not ATOM records, PDB header with TLS >> records that sometimes may be lost or manipulated and specific >> converting programs to add TLS contribution). Also note, that not all >> programs extract TLS information from PDB header to compute R-factors, >> but ALL programs can read ATOM records. > > As you have stated this, it is not true. The big plus with TLS is that it > models anisotropic displacements, which are not described in ATOM lines. > You would need to include the (derived) ANISOU lines to reproduce > R-factors. I bring this up again, because I feel undue respect is given to > the total B factor (I have heard it called the "true" B factor - I have no > idea what kind of truth that is!). > > Anyway, these are all different representations of the same thing, and > should work equally well so long as you know which you are using. The > scariest thing from the last thread was that our attempt to document it > with a REMARK 3 line is being stripped by the RCSB. > > Cheers > Martyn >
