Hi John,
I was wondering if there is an easy way to take the output from TLSmd and input the definitions into phenix.refine.
Unfortunately, I do not know since it never happened to me to use it. It is our long term plan to implement our own automatic TLS domains identification option.
If any one has an example file of a phenix TLS file with multiple TLS definitions per chain I would love to have it (The manual just gives an example of TLS definitions of one per chain, but I am getting confused on how to define mutlitple).
I'm loading two files at the web address below: one with TLS selections for multiple groups, another one is the PDB file with refined model and TLS records in its header. This is actually the most complex selection for TLS groups I ever used -:) http://cci.lbl.gov/~afonine/tls_selections/ Please let me know if you have any more questions. Pavel.