[phenixbb] fwd: TLS without isotropic adp refinement

[Pavel Afonine]

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 <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
>
>
>
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> phenixbb at phenix-online.org
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>   
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