Thanks Pavel. I was a little tired from an overnight Synchrotron run when I wrote that. Lesson: Stay off the internet when you are tired. Haha. I forgot that the TLS groups would be assigned per chain not per molecule. Thanks for the correction. I didn't know you could run find TLS groups as part of the refinement strategy. Very helpful.
-Yarrow On Tue, Apr 15, 2014 at 8:36 PM, Pavel Afonine <[email protected]> wrote: > Hello Yarrow, > > in some refinement software (phenix.refine), if you run TLS refinement and >> you don't specify the TLS groups, the entire structure is considered one >> TLS group > > > if you use TLS parameterization and do not specify TLS groups, two > scenarios are possible: a) each chain will be treated as one TLS group, b) > if you define tls.find_automatically=true (or check appropriate box in the > GUI) it will find TLS groups as part of refinement similarly to TLSMD but > ~100 times faster. > > >> This may be why the annotators could not find the TLS groups. > > > In any case, if TLS refinement was used, then TLS matrices defining > refined TLS parameters are always present in PDB file header (in REMARK 3 > records). In case of just one group there will be just one set of T,L and S. > > Finally, if you've done TLS refinement and decided not to use TLS in the > next refinement you do not need to remove ANISOU records manually - the > program will figure this out. > > All the best, > Pavel > >
