[phenixbb] ADP group definitions

[Pavel Afonine]

Hi Roeland,

yes, it is possible to refine isotropic individual B-factors, group 
B-factors and TLS in any combination for any part of the model. I'm not 
sure what's happening in your case. The set of parameters below looks ok 
to me.

Here is what I did:

1) I copied your parameters below into a "par" file and run this command:

phenix.refine --diff-params par > params

2) Then I added "group_adp_refinement_mode=.." keyword to it.

I'm attaching the "params" file. Could you please try to run the 
refinement again using this file? Please make sure you are using the 
latest version of PHENIX.

Please let me know if this fixes the problem.

Pavel.

PS> Are you sure you don't want to use "individual_adp" ?



On 3/9/09 3:37 AM, Roeland Boer wrote:
> Dear all,
>
> I have a question regarding the definition of the ADP groups. I'm 
> refining a structure using a different isotropic B for each domain, 
> while applying TLS for some mobile domains (I'm also using NCS 
> restraints for all equivalent domains). In the refinement log file, 
> however, the isotropic B of the domains refined with TLS, as reported in 
> the "TLS refinement" section, is equal to the B of the starting model in 
> all refinement macro cycles. It seems, therefore, that the isoB for the 
> TLS groups in not refined, although I've included these domains in the 
> .adp.group definitions (the log file actually confirms that there are 7 
> adp groups). Is it possible to refine TLS and isotropic B's on the same 
> part of a model?
>
> I include the input file below.
>
> Thanks for any suggestions,
> Roeland Boer.
>
>
> refinement.input.xray_data.labels=F
> refinement.refine.strategy=tls+individual_sites+group_adp
> refinement.refine.adp.tls="chain A and resid 4:132"
> refinement.refine.adp.tls="chain B and resid 4:132"
> refinement.refine.adp.tls="chain C and resid 4:132"
> refinement.refine.adp.tls="chain X and resid 4:132"
> refinement.refine.adp.tls="chain Y and resid 4:132"
> refinement.refine.adp.tls="chain Z and resid 4:132"
> refinement.refine.adp.one_adp_group_per_residue=False
> refinement.refine.adp.group="resid 133:203"
> refinement.refine.adp.group="chain A and resid 4:132"
> refinement.refine.adp.group="chain B and resid 4:132"
> refinement.refine.adp.group="chain C and resid 4:132"
> refinement.refine.adp.group="chain X and resid 4:132"
> refinement.refine.adp.group="chain Y and resid 4:132"
> refinement.refine.adp.group="chain Z and resid 4:132"
> refinement.main.number_of_macro_cycles=4
> refinement.input.xray_data.low_resolution=20.0
> refinement.input.xray_data.high_resolution=3.4
> refinement.main.ncs = True
> refinement.ncs.find_automatically = False
> refinement.ncs.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
> }
> refinement.ncs.restraint_group {
>   reference = chain B and resid 4:132
>   selection = chain A and resid 4:132
>   selection = chain C and resid 4:132
>   selection = chain X and resid 4:132
>   selection = chain Y and resid 4:132
>   selection = chain Z and resid 4:132
> }
> refinement.output.prefix=test
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>