Hi Dirk,

thanks a lot for your feedback.

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If you refine a macromolecular structure with phenix.refine using TLS and isotropic B-factors, the resulting PDB file will have the effective isotropic B-factors and their anisotropic corrections as ANISOU cards from both the TLS components and the individual isotropic B-factor component.

Just to make this sure once again. phenix.refine always writes out the total B-factors and not split them. The total B-factor in phenix.refine is defined as: Utotal = Utls + Ulocal + Ucryst. So, the ANISOU records always contain Utotal and ATOM records contain isotropic equivalent of Utotal which is trace(Utotal)./10000*8*pi**2/3 (correct me if I missed a scale somewhere).

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I think, this is very useful, because the PDB file has the informations about the various B-factor components readily available, both for non-crystallographers that are not aware of TLS and for reproducing refinement results with other software.

This is what I had in mind. Plus, all the information about B-factors is in ATOM and ANISOU records so: 1) you don't need any external programs to put things together; 2) you can load your structure say into PyMol and color it by B-factors, 3) you don't need to rely on PDB file header: if you loose it you don't loose much of the information, etc...

Also, the latest development CCI Apps (http://www.phenix-online.org/download/) has a new tool: phenix.tls that allows you to go back and forth between both representations: total and residual B-factors. It will be available in the next general PHENIX release.

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However, if such a PDB file is fed into another refinement run with phenix.refine, the program recognizes the ANISOU cards and automatically switches to individual anisotropic B-factor refinement, unless you explicitly state, that you wish to continue with isotropic B-factor refinement by giving, for instance, a command line keyword like adp.individual.isotropic=all or convert_to_isotropic=true (see here).

Yes, it was in the past. Now it tries to be smarter about it. See below.

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I think, this is not reasonable, since the vast majority of macromolecular structures is refined at resolutions that do not justify anisotropic B-factor refinement, and most users simply use the default refinement parameters and are probably not aware of this behaviour.

I agree. See below.

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May I therefore suggest to the developers of phenix to revert this behaviour, such that isotropic B-factor refinement is the default and anisotropic B-factor refinement is only done, if the user explicitly states that she/he wants it?

In the latest version (http://www.phenix-online.org/download/) the default behavior of phenix.refine is (if no TLS is used):

- isotropic atoms in input PDB file are refined with isotropic ADP;
- anisotropic atoms in input PDB file are refined as individual anisotropic if resolution is "high enough";
- anisotropic atoms in input PDB file are converted to isotropic and then refined as individual isotropic if resolution is not "high enough".

The decision about whether the resolution is "high enough" or not is made using this parameter:
switch_to_isotropic_high_res_limit=1.7
Of course a user can overwrite it by setting it to the value he/she likes.

If TLS is used: all atoms participating in TLS groups start having (or keep having) anisotropic component.

I hope this clarifies things a little bit!

Pavel.