Hi again and thanks for your answers. I have been considering your comments and as I see it I have three options A) Leave the pdb with no TLS refinement, as I already have good R values without them. B) Perform the TLS refinement and not worry about the high B-factors since it is normal that they increase in this step. C) Use TLSanl with BRESID=TRUE. This mantains the B-factors as before the TLS while still adding the ANISOU component to the file.
Obviously, option C is the one that gives the best results (B and Rfactors) but I have some doubts about it: Why is the default in TLSanl set to BRESID=FALSE? Since the default in REFMAC is not to specify TLSOUT ADDU, should I run TLSanl defining BRESID=TRUE for every pdb from now on? Thanks, Carles El 05/06/2014, a les 19.58, Tim Gruene <[email protected]> va escriure: > Dear Carles, > > it used to be the case (and probably still is) that you had to specify > BRESID false > > when using tlsanl with a PDB file from refmac5. It seems that 'TLSOUT > ADDU' specified for refmac5 allows you to use tlsanl with its default > value 'true'. > > The incorrect mixture might lead to an artifical increase or decrease of > Biso. > > Best, > Tim > > On 06/05/2014 05:51 PM, Carles Palanca i García wrote: >> >> >> >> >> >> >> P { margin-bottom: 0.21cm; } >> >> >> Hello, >> >> I'm almost done refining a protein-DNA >> complex at 3A, but when I apply TLS (Refmac+TLSanl to include the >> ANISOU component) the B factors increase from 50-60 to 100-110 A2. >> The crystal is a bit special since it has 80% of solvent and the >> Wilson B-factor is 87 A2. When I compare my Bfactors with other >> structures of similar resolution using Phenix Validation, my data is >> clearly an outlier. >> >> >> To perform the TLS refinement I have >> generated .tlsin files for 2,4 and 6 groups with the TLSmd server and >> used them in refmac jobs consisting of 20 cycles of TLS refinement+50 >> cycles of restrained refinement. This way the R-factor and R-free >> values have drop 1-2% (before it was 22.3/24.1). The three different >> options suffer from the same problem regarding high B-factors after >> TLSanl. Am I doing something wrong during the TLS refinement? What >> can I do to preserve the original Bfactors? >> >> >> Thanks in advance, >> >> Carles Palanca. >> >> >> > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A >
