Hi Bryan,
let me try a simpler question : do the TLS results need to be transformed or scaled somehow so they are on the same basis as the ones from refmac/tlsanl/anisoanl (i know this is partially a ccp4 question)?
I wrote most (if not all) TLS related code in phenix. Unfortunately, I can't answer your questions because I do not know which transformations the above programs do, which units, origins and scales they use, and even what they do (speaking of the last two). So, I afraid I'm useless here... I'm sure there must be a thing or a number of things somewhere like a scale factor such as units for L (degrees**2 or radians**2), or 8*pi**2*something in U conversions, or different origin, etc ... I recall I had to figure out myriads of things like this before TLS started working in phenix.refine. Typically these "obvious" details are never mentioned in general papers as probably "too technical". This is why it is rarely not tricky to jump between the programs. It's probably like if you take two different cars (different makes and models) that both function well and sound, and then swap their engines without thinking too much, then the chances are that both will stop working. Let do something practical to address this... What I can do for you is: if you clearly explain me what exactly you are trying to achieve then I just simply add the corresponding functionality to PHENIX and then you (and potentially other PHENIX users) will be able to do what you want within one self-consistent framework, and avoiding jumping between units, conventions and other hidden meanings. Of course this might take some time - from a couple of days to a week, so you would need to wait a little bit, but then you will have a tool in hands to use any time you want. So, let me know.
p.s: new subscription address : slow to appear on bulletin board...?
Not sure what you mean ? Pavel.