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 component; - 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. Pavel