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 <[log in to unmask]> 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
>
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