[phenixbb] fwd: TLS without isotropic adp refinement

Nathaniel Echols NEchols at lbl.gov
Thu Mar 5 10:00:00 PST 2009


(I think the server must have a lag time between adding a new email  
address and accepting posts from it. . .)

> From: Roeland Boer <rbocri at ibmb.csic.es>
> Date: March 5, 2009 5:29:19 AM PST
> To: phenixbb at phenix-online.org
> Subject: TLS without isotropic adp refinement
>
> Dear all,
>
> I'm trying to refine a structure using TLS on some of the domains  
> without refining the isotropic B factors of the atoms of the full  
> structure. I haven't been able to do this: the isotropic B factors  
> seem to be refined per residue when I include TLS. If I don't use  
> TLS, the B factors are not refined. I've looked around in the  
> archives and browsed the manual without luck. Any suggestions would  
> be highly appreciated. I include the parameter file I've used.

Quoting Pavel (since he's teaching a workshop): "phenix.refine always  
writes out the total B-factors and not split them. The total B-factor  
in phenix.refine is defined as: Utotal = Utls + Ulocal + Ucryst."  So  
the atomic B-factors in your structure are not being refined  
individually, but they change anyway because the contribution of the  
TLS refinement is included.

-Nat

>
> Kind regards,
> Roeland Boer.
>
>
> ++++++++++++++ Parameters ++++++++++++++++
>
> refinement.main.number_of_macro_cycles=4
> refinement.main.ncs = True
> refinement.input.xray_data {
> labels=F
> low_resolution=20.0
> high_resolution=3.6
> }
> refinement.refine {
> strategy=tls+individual_sites
> adp {
>   tls="chain A and (resid 4:132 or resid 301)"
>   tls="chain B and (resid 4:132 or resid 301)"
>   tls="chain C and (resid 4:132 or resid 301)"
>   tls="chain X and (resid 4:132 or resid 301)"
>   tls="chain Y and (resid 4:132 or resid 301)"
>   tls="chain Z and (resid 4:132 or resid 301)"
> }
> }
> refinement.ncs {
> find_automatically = False
> restraint_group {
>   reference = chain A and resid 133:203
>   selection = chain B and resid 133:203
>   selection = chain C and resid 133:203
>   selection = chain X and resid 133:203
>   selection = chain Y and resid 133:203
>   selection = chain Z and resid 133:203
> }
> restraint_group {
>   reference = chain B and (resid 4:132 or resid 301)
>   selection = chain A and (resid 4:132 or resid 301)
>   selection = chain C and (resid 4:132 or resid 301)
>   selection = chain X and (resid 4:132 or resid 301)
>   selection = chain Y and (resid 4:132 or resid 301)
>   selection = chain Z and (resid 4:132 or resid 301)
> }
> }
> refinement.output.prefix=3.6-tlsnter-indsite-inputb-autowght-ncs
> -------------------- Parameters --------------------------
>
>

-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov






More information about the phenixbb mailing list