On Saturday, 20 April 2013, Nat Echols wrote:
> On Sat, Apr 20, 2013 at 6:51 PM, Jinzhong Lin <[email protected]> wrote:
>
> > On 04/20/2013 09:03 PM, Ethan A Merritt wrote:
> >
> >> I really disapprove of the idea of writing out ANISOU records to
> >> describe TLS refinement. Notwithstanding the fact that the PDB
> >> recommends this, I strongly suggest that you tell refmac_not_
> >> to write out ANISOU records. The TLS model is adequately
> >> described in the header, the extra ANISOU records are a less
> >> good way of describing the same thing.
> >>
> >
> This would make sense if there was a standardized format for TLS which all
> programs that might care had implemented - which there isn't, as far as I
> know.
That is correct. There ought to be.
This is far from the first time I've ranted on the subject.
What is really needed is a "TLS group" field in the ATOM record so that
each atom is unambiguously associated with a TLS group that
describes its displacement. No separate ANISOU needed or wanted.
[aside: I know that phenix can refine individual aniso ADP components
on top of the TLS, but IMNHSO this is not a correct thing to do].
> As a result there are many entries in the PDB whose TLS records
> cannot be easily interpreted. A further problem is that not every program
> outputs REMARK records where TLS information is usually dumped, but most
> will preserve ANISOUs.
That, I believe, is false. There is no program that refines TLS
groups without writing out the refined parameters in the output
file.
> Finally, most molecular graphics programs don't
> have an option to visualize TLS parameters, but most do support anisotropic
> ellipsoids.
That is fixable :-)
Ethan
> I agrees with you. But I am using phenix for the refinement, unfortunately
> > there is no option for it not to write the ANISOU records.
> >
>
> Since I assume you don't actually care about the ANISOUs for the purpose of
> adjusting your model in Coot, I suggest this:
>
> grep -v ANISOU model.pdb > model_iso.pdb
>
> You're going to start the next round of refinement with higher R-factors
> than if the ANISOUs were left alone, but in my experience they'll usually
> recover if you run TLS refinement again.
>
> -Nat
>
