Just to add to Nat's reply (which is 100% correct): even when you refine group B-factors and nothing else, the mutual distribution of B-factors withing the group remains the same but it is a constant correction that is the refinable parameter.

For example, if for residue A the B-factors before group-B refinement were: 5,6,7,8.
Then after group-B refinement they can be 7,8,9,10 or 2,3,4,5; where in the first case the individual overall B-factor correction was 2 and in the second case it was 3.

Cheers,
Pavel.


On 3/5/09 10:00 AM, Nathaniel Echols wrote: 
(I think the server must have a lag time between adding a new email  
address and accepting posts from it. . .)

  
From: Roeland Boer <[email protected]>
Date: March 5, 2009 5:29:19 AM PST
To: [email protected]
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
[email protected]



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