Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

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Subject: Re: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
From: Ulrich Baumann ulrich {- dot -} baumann {- at -} IBC {- dot -} UNIBE {- dot -} CH
Date: 2008-03-13

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Subject: Re: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-03-13

Subject: Re: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-03-13

Hi Dale,

to my knowledge, sfcheck calculates the contribution of the bulk
solvent using the double-exponential scaling model (Babinet model),
but not using the mask model that REFMAC applies per default. I
sometimes have to discuss similar R-factor differences with RCSB upon
PDB submission of refined models ...

Best regards,

Dirk.

Am 12.03.2008 um 22:20 schrieb Dale Tronrud:

> Hi,
>
> I am looking over a number of models from the PDB but have been
> unable to reproduce the R-factors for any model that was refined
> with Refmac and contains TLS parameters. I usually can't get within
> 5% of the reported value. On the other hand, I usually do pretty
> well for models w/o TLS.
>
> An example is the model 1nkz. The PDB header gives an R value
> of 17% but even when I use tlsanal in CCP4i to generate a PDB with
> anisotropic B's that mimic the TLS parameters I get an R value of
> 22.4% using SFCheck. (I'm not implying that I suspect any problem
> with 1nkz, in fact I have every reason to believe this is the great
> model its published stats indicate.)
>
> I've found a CCP4 BB letter that stated that SFCheck does not
> pay attention to anisotropic B's but that letter was dated 2002.
> I hope this limitation has been removed, or at least the output
> would mention this limitation.
>
> Setting up a refinement in Refmac involves a large overhead,
> since even for zero cycles of refinement the program insists on
> a complete stereochemical definition for the strange and wondrous
> groups in this model. I would just like to verify the R factor
> and calculate a proper map for inspection in Coot. Since I have
> many models I would like to look at, I would like a simple procedure.
>
> I did set up a Refmac run for another model, for which I do
> have all the .cif's required, but even after refinement I was not
> close to the reported R.
>
> I see that the models I'm interested in are not present in the
> Electron Density Server, so I suspect I'm not alone in fighting
> this battle.
>
> Any advice would be appreciated,
> Dale Tronrud

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Dirk Kostrewa
Gene Center, A 5.07
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