[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
>>
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>
>> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>>
>>
>>
>>
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---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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