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. . .)

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From: Roeland Boer 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

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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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