[phenixbb] phenix.refine : desire less conservative bonds and angles in optimize_wxc = True.

[Pavel Afonine]

  Hi Francis,

both bond and angle rmsds did not change much for a broad range of 
target weight scales - from 0.5 to 10: for all trial values they stayed 
approximately the same 0.001/0.4.  Interestingly, the Rfree did change 
much too, although it keeps slightly dropping till wxc_scale=10.
Hm... first of all, this is a bit unusual so I wonder if there is 
anything special about your data/model? Also, I wonder what if we let 
the procedure go beyond wxc_scale=10? Unfortunately, it's not a 
parameter and "10" is hardwired somewhere in the code... But if you send 
me the data and model I will be able to change the code and try it myself.

Alternatively, you can just try manually a few values, like wxc_scale= 
15, 20, 25, .. until it stops making sense -:)

Pavel.


On 1/18/11 12:35 PM, Francis E Reyes wrote:
> Although I specify that I'll allow a max angle rmsd of 2.0 
> (angles_rmsd_max), optimize_wxc = True results in a limited range of 
> angles.. for example my optimize_wxc output
>
>
> Start r_work= 0.2507 r_free= 0.2709 bonds= 0.002 angles=  0.47
>       r_work= 0.2558 r_free= 0.2728 bonds= 0.001 angles=  0.41 scale=  
> 1.00
>       r_work= 0.2550 r_free= 0.2725 bonds= 0.001 angles=  0.41 scale=  
> 1.40
>       r_work= 0.2543 r_free= 0.2724 bonds= 0.001 angles=  0.41 scale=  
> 1.80
>       r_work= 0.2538 r_free= 0.2723 bonds= 0.001 angles=  0.41 scale=  
> 2.20
>       r_work= 0.2533 r_free= 0.2721 bonds= 0.001 angles=  0.42 scale=  
> 2.60
>       r_work= 0.2529 r_free= 0.2721 bonds= 0.001 angles=  0.42 scale=  
> 3.00
>       r_work= 0.2525 r_free= 0.2721 bonds= 0.001 angles=  0.42 scale=  
> 3.40
>       r_work= 0.2520 r_free= 0.2720 bonds= 0.001 angles=  0.42 scale=  
> 3.80
>       r_work= 0.2516 r_free= 0.2719 bonds= 0.001 angles=  0.43 scale=  
> 4.20
>       r_work= 0.2513 r_free= 0.2719 bonds= 0.001 angles=  0.43 scale=  
> 4.60
>       r_work= 0.2510 r_free= 0.2718 bonds= 0.001 angles=  0.43 scale=  
> 5.00
>       r_work= 0.2501 r_free= 0.2717 bonds= 0.002 angles=  0.44 scale=  
> 6.00
>       r_work= 0.2494 r_free= 0.2718 bonds= 0.002 angles=  0.45 scale=  
> 7.00
>       r_work= 0.2488 r_free= 0.2716 bonds= 0.002 angles=  0.46 scale=  
> 8.00
>       r_work= 0.2481 r_free= 0.2715 bonds= 0.002 angles=  0.46 scale=  
> 9.00
>       r_work= 0.2476 r_free= 0.2714 bonds= 0.002 angles=  0.47 scale= 
> 10.00
>       r_work= 0.2561 r_free= 0.2729 bonds= 0.001 angles=  0.41 scale=  
> 0.85
>       r_work= 0.2563 r_free= 0.2729 bonds= 0.001 angles=  0.41 scale=  
> 0.70
>       r_work= 0.2567 r_free= 0.2730 bonds= 0.001 angles=  0.42 scale=  
> 0.55
> Final r_work= 0.2476 r_free= 0.2714 bonds= 0.002 angles=  0.47
>
>
> The resolution is about 1.95A and I think the angles/bonds are a 
> little too tight.
>
> My wxc_scale is currently set to 0.01. Does optimize_wxc use this as a 
> starting point/does it matter what this value is set to when 
> optimize_wxc =True ? Is the scale= result in the output really wxc_scale?
> Thanks!
>
> F
>
>
> ---------------------------------------------
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
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