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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: R Michael Garavito garavito {- at -} MSU {- dot -} EDU
Date: 2008-03-12

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Subject: Re: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
From: Ramaswamy rams {- at -} POORI {- dot -} BIOCHEM {- dot -} UIOWA {- dot -} EDU
Date: 2008-03-12

Subject: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-03-12

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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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Color of heme containing Xtals
From: R Michael Garavito garavito {- at -} MSU {- dot -} EDU
Date: 2008-03-12