Hi Bryan,
thanks, phenix.tls looks helpful.
oh, good, I'm glad you find it helpful!
.... and if the input pdb has derived anisou/B's, could this potentially interfere in the TLS protocol? i.e. would it be wiser to simply reset them every time?
It shouldn't really matter for phenix.refine. Probably it's better if you feed in a PDB file with total B-factors in rather than residual, but honestly I wouldn't expect any significant difference. Of course, if you want to have a rock solid answer then just try using both approached and compare the difference.
i know ADP's/Bisos are derived from TLS matrices,
Only TLS component is derived from TLS matrices. This is explained here: http://www.phenix-online.org/newsletter/CCN_2010_07.pdf see article "Atomic Displacement Parameters (ADPs), their parametrization and refinement in PHENIX". Pavel.