[ccp4bb]: forwarded questions on R factors from refmac and sfcheck

["M.D.Winn" <M.D.Winn@dl.ac.uk>]

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DON'T REPLY TO ME!!!

Message from "Tom Lee" <tomlee@msg.ucsf.edu> that got trapped
in ccp4bb problems:

> Hi,
> 
> I have a question regarding Refmac5 and Sfcheck.  I used Refmac5 with =
> TLS refinement.  After Refmac5, I run TLSANL to add TLS contributions to =
> the isotropic B factors as well as to add "ANISOU" lines for anisotropic =
> B factors.  Please correct me if I'm wrong.  My questions are:
> 
> 1. When I run SFCHECK on the output pdb of TLSANL, it calculates R =
> factors ~2% higher than those from Refmac5 output.  I think part of this =
> is because SFCHECK does not use ANISOU records to calculate Rs.  Is =
> there a way to include anisotropic B factors when calculating R factors?
> 
> 2.  Are there other reasons that result in the difference in the R =
> factors from Remac5 and Sfcheck?  If I delete the ANISOU records from =
> the output of TLSANL and use the resulting pdb as input pdb for another =
> round of Refmac5 (thus no ansiotropic TLS contributions,  just for =
> checking R factors), I notice the starting R factors is only ~1% higher =
> than those from previous Refmac (with TLS), but still ~1% lower than =
> those from Sfcheck.  One reason I can think of is that maybe Sfcheck =
> uses a different way in scaling and bulk solvent correction.  But it =
> seems to me the difference shouldn't be
> so big.
> 
> 3. What criteria do people use to judge whether to report anisotropic B =
> factors?  Only with very high resolution?  I only have 1.9 A data, if I =
> leave them out, what R factors should I report, those from Remac5 or =
> those from Sfcheck?
> 
> Tom Lee
>