[phenixbb] refinement

Thu Dec 10 22:43:59 PST 2009

Please upgrade to the latest version of Phenix - 1.5-2.

On Dec 10, 2009, at 9:56 PM, Pei-Chun Lin wrote:

> Hi,
>
> Thanks for answering my previous question about weight adjustment,  
> but I have a new problem.
>
> If I use,
>
> ordered_solvent=true simulated_annealing=true \
> strategy=rigid_body+individual_sites+individual_adp \
> main.number_of_macro_cycles=10 \
> output.prefix=best_model --overwrite
> the program run fine and give the result: Start R-work = 0.4713, R- 
> free = 0.4786, Final R-work = 0.2721, R-free = 0.3769
>
>
> However, when I tried to change weight,
>
> ordered_solvent=true simulated_annealing=true \
> strategy=rigid_body+individual_sites+individual_adp \
> optimize_wxu=true optimize_wxc=true \
> main.number_of_macro_cycles=10 \
> output.prefix=best_model --overwrite
>
> the program show error message,
>
> ---------xray term weight optimization (wxc)----------
>
> Traceback (most recent call last):
>   File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/ 
> refine.py", line 5, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/ 
> command_line.py", line 82, in run
>     call_back_after_monitor_collect=call_back_after_monitor_collect)
>   File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/ 
> driver.py", line 1143, in run
>     call_back_after_monitor_collect = call_back_after_monitor_collect)
>   File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/ 
> strategies.py", line 449, in refinement_machine
>     log                           = log)
>   File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/ 
> weight_xray_chem.py", line 256, in __init__
>     self.wxc_optimization()
>   File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/ 
> weight_xray_chem.py", line 511, in wxc_optimization
>     wxc = self.holder.wxc
> AttributeError: weight instance has no attribute 'holder'
>
>
> How do I fix this?
>
>
> PC
>
>
> Date: Thu, 10 Dec 2009 08:31:25 -0800
> From: PAfonine at lbl.gov
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] refinement
>
> Hi Pei-Chun,
>
> the target function for coordinates refinement that is used in  
> phenix.refine is following:
>
> T = wxc_scale * wxc * Txray + wc * Trestraints
>
> where: wxc is determined automatically, wc =1 by default, and  
> wxc_scale = 0.5 by default. A user can adjust wxc_scale or wc.
>
> Responding your question about "put much more weight on geometry  
> restraints": you can do it either by decreasing wxc_scale or by  
> increasing wc. I would try an array of values for wxc_scale to see  
> which one gives the best result.
>
> Please let me know if it's still not clear or if you have any other  
> questions!
>
> Pavel.
>
>
> On 12/10/09 7:38 AM, Pei-Chun Lin wrote:Hi,
>
> When talking about "put much more weight on geometry restraints to  
> avoid overfitting", what wxc and wxu value will you suggest to use  
> for a 4A structure?
> I am working on a 3.5A structure and have no experience of adjusting  
> weight value before. Any suggestion will be very helpful to me.
>
>
> PC
>
>
> Date: Tue, 8 Dec 2009 20:12:29 -0800
> From: PAfonine at lbl.gov
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] refinement
>
> Hi,
>
> although I've seen cases like yours when SA in Cartesian space did  
> miracles, in many of cases modeling at 4A resolution is a tough  
> problem.
>
> Since clearly SA didn't work out (given R/Rfree ~ 37/50% and the  
> starting 48/50), I would try splitting your model into rigid domains  
> and refine each as a rigid body. Plus, I would refine one isotropic  
> B per residue or per domain (try both). This is a few minutes to try  
> so why don't you do so.
> Also, I would still combine it (rigid body and B-factor refinement)  
> with Cartesian SA, but I would put much more weight on geometry  
> restraints to avoid overfitting.
>
> As you probably aware of, in phenix.refine you can run combined  
> refinement jobs, for example, consisting of SA, rigid body, B-factor  
> refinement and so on. So I would recommend playing with the above  
> suggestions to see if it works. Plus, don't forget looking at the  
> maps - may be you manage to fit something manually.
>
> By the way, which R-factors you get if you run:
>
> phenix.model_vs_data data.mtz model.pdb
>
> (phenix.model_vs_data will account for twinning (if any) using  
> Xtriage automatically) ?
>
> Write us if you have questions.
>
> Good luck,
> Pavel.
>
>
>
> On 12/8/09 7:02 PM, r n wrote:
> Thanks a lot. I did download the new -dev249 and did cartesian SA, R  
> goes down to 37 but R-free (50) did not.
> Any suggestions?
>
>
>
> From: Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov>
> To: phenixbb at phenix-online.org
> Sent: Tue, December 8, 2009 3:34:09 PM
> Subject: Re: [phenixbb] refinement
>
> > I do have very low resolution data (around 4 ang), what are
> > the efficient way of doing refinement, either rigid body alone or
> > rigidbody and tls or individual with group_adp. I did both, but not
> > much significant changes in Rfree stays around 48/50%.
>
> You could also try Cartesian or torsion-angle simulated annealing.
> I'd try both. In my experience Cartesian SA often works better even
> at low resolution.
> If you get errors running torsion-angle annealing, please try
> the latest nightly build (dev-249) since I've fixed several
> problems since the 1.5-2 release.
>
> > Also I do have other questions
> >
> > 1. While doing rigid body refinement, phenix complaint about the
> > special position and could not perform rigid body refinement,
> > whereas individual site refinement is working fine. I do have to
> > delete the atom in special position for rigid body refinement?
>
> You could use
>   sites.rigid_body = ...
> to select the bodies you want to refine. The rest (including your
> atom on the special position) will not move.
>
> Ralf
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Berkeley Lab
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