refine : a priori TLS tensor eigenvalues
[ phenix 1.6.4-486 ] i gather that phenix.refine will not take a priori refined TLS tensor eigenvalues - either from input or from the pdb header. is this right? -bryan
Hi Bryan,
[ phenix 1.6.4-486 ]
i gather that phenix.refine will not take a priori refined TLS tensor eigenvalues - either from input or from the pdb header. is this right?
phenix.refine does not use TLS information from PDB file header, simply because in general phenix.refine "does not trust things" under REMARK records (there are good reasons for this, which I will not mention now since it is not a subject of this conversations). Only phenix.model_vs_data and phenix.tls uses this information. phenix.refine has powerful algorithms to recompute TLS parameters from just model and data files, and user provided selections for TLS groups. Pavel.
thanks, phenix.tls looks 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? i know ADP's/Bisos are derived from TLS matrices, but a clarification about what to start with would be helpful. -bryan
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.
participants (2)
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Bryan Lepore -
Pavel Afonine