[phenixbb] phenix.refine : desire less conservative bonds and angles in optimize_wxc = True.
Pavel Afonine
pafonine at lbl.gov
Tue Jan 18 12:59:08 PST 2011
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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>
>
>
>
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