[phenixbb] Questions on TLS output and more info on phenix.tls
pafonine at lbl.gov
Mon May 29 20:11:16 PDT 2017
> (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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