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

Francis E Reyes Francis.Reyes at Colorado.EDU
Tue Jan 18 15:12:44 PST 2011


Pavel I'm still refining against experimental phases.. would that  
matter? The reason I ask is because in my 2fofc maps, there's density  
that can possibly be accommodated by not being so strict in the  
backbone (this is a nucleic acid).



F

On Jan 18, 2011, at 1:59 PM, Pavel Afonine wrote:

> 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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>>
>>
>>
>>
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---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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