hello all- i apologize if this question has previously been posted, but i was not able to track down an answer by google. i am refining a 2.75A structure that has three copies of the protein in the asu with phenix 1.4-3 and using NCS with each chain as an NCS group. after molecular replacement, i set all of the b-factors to the wilson b-factor and then performed four different refinements: grouped b-factor (1 group per residue) : Rwork 22.6 Rfree 27.0 individual b-factor : Rwork 21.4 Rfree 26.6 grouped b + tls ( : Rwork 21.9 Rfree 25.2 individual + tls : Rwork 21.2 Rfree 24.8 i defined the tls groups with the following: adp { tls = chain A tls = chain B tls = chain C } after grouped b-factor the atoms of each residue all have the same b- factor as i expected. after grouped b-factor+tls, however, each atom of a residue has a unique b-factor, which i did not expect. i realize that this confusion is likely caused by me not fully understanding how tls refinement is implemented. if someone could explain this to me, i will be able to sleep better. thank you for your time, jeff Jeffrey Chao, PhD 1300 Morris Park Ave ASB-Golding 601 Bronx NY 10461 [email protected] 718-430-8597
On 27 Jan 2009, at 16:10, Jeffrey Chao wrote:
hello all- i apologize if this question has previously been posted, but i was not able to track down an answer by google. i am refining a 2.75A structure that has three copies of the protein in the asu with phenix 1.4-3 and using NCS with each chain as an NCS group. after molecular replacement, i set all of the b-factors to the wilson b-factor and then performed four different refinements: grouped b-factor (1 group per residue) : Rwork 22.6 Rfree 27.0 individual b-factor : Rwork 21.4 Rfree 26.6 grouped b + tls ( : Rwork 21.9 Rfree 25.2 individual + tls : Rwork 21.2 Rfree 24.8 i defined the tls groups with the following: adp { tls = chain A tls = chain B tls = chain C } after grouped b-factor the atoms of each residue all have the same b- factor as i expected. after grouped b-factor+tls, however, each atom of a residue has a unique b-factor, which i did not expect.
This has to do with the way that phenix output the Bs (another debate...) Phenix outputs the total B, including the contribution to TLS. A simple way to think about it, is that since the TLS tensor has an origin, its contribution to each different atom is space is different. Thus, even if atoms have a grouped B factor (same for the group) the TLS for that chain will contribute different to each atom and the output total B will be different (but not dramatically for atoms close to each other)
i realize that this confusion is likely caused by me not fully understanding how tls refinement is implemented. if someone could explain this to me, i will be able to sleep better. thank you for your time, jeff
bed time reading: "Use of TLS parameters to model anisotropic displacements in macromolecular refinement" http://scripts.iucr.org/cgi-bin/paper?S0907444900014736 A.
Jeffrey Chao, PhD 1300 Morris Park Ave ASB-Golding 601 Bronx NY 10461 [email protected] 718-430-8597
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Anastassis Perrakis -
Jeffrey Chao