[phenixbb] Questions on TLS output and more info on phenix.tls

Pavel Afonine pafonine at lbl.gov
Mon May 29 20:11:16 PDT 2017

Hi Michael,

> (1) Just to be sure, I looked for the definition of what is written in 
> the ATOM records of the output PDB file after refinement with TLS: 
>  residual B or total B (residual B + TLS contribution). I always 
> thought the latter after refinement with TLS, but nothing was 
> explicitly stated.

ATOM records contain isotropic equivalent of total ADP (individual 
+TLS), and corresponding ANISOU records contain full ADP as it is.

> (2) Also, I have looked for it extensively in the Phenix 
> documentation, I have not found any information on phenix.tls, even 
> though in several places (e.g., phenix.ensemble_refinement), there are 
> explicit references to phenix.tls:  “If TLS is used the TLS components 
> must be present in the atom records (see phenix.tls)”  The information 
> from just doing % phenix.tls -h does not give enough insight into 
> options and there use.
> Can someone point me to the right place to get these answers?

phenix.tls is a simple tool to
- split total ADP in ATOM and ANISOU records into residual and TLS 
- assemble total ADP from residual and TLS component.

Let me know what exactly you are trying to do and I will tell how.

Yes, we need to improve docs on this one.


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