[phenixbb] Weight optimization

[Frank von Delft]

Hi Pavel -- are those the default targets?  Because I've never figured 
out why phenix.refine consistently comes up with much lower bond-rmsd 
(0.05-8) than what I thought should be aimed for (0.018ish for high res 
data -- there are many long ccp4bb threads about this in the archive).

phx.



On 25/05/2010 23:45, Pavel Afonine wrote:
> Hi Jianghai,
>
> try adjusting these values to match your expectations:
>
>  target_weights {
>    bonds_rmsd_max = 0.05
>    angles_rmsd_max = 3.5
>  }
>
> I've never really played with this, but this is done exactly to 
> address your question. That weight will be selected that minimizes the 
> Rfree and obeys the above limits. I'm not sure what happens if you 
> already start with the values that are higher than these limits.
>
> Please let me know if you have any problems with this.
>
> Pavel.
>
>
> On 5/25/10 9:08 AM, Jianghai Zhu wrote:
>> Hi,
>>
>> I am using the optimize_wxc=true and optimize_wxu=true in my last 
>> refinement.  The R and Rfree went down but the RMSDs were way too 
>> large. I wonder if phenix.refine still targets the geometry when it 
>> optimizes the R and Rfree.  Here are the results from almost two 
>> identical runs except the weight optimization.
>>
>> 1) optimize_wxc = False  optimize_wxu = False wxc_scale=0.08 
>> wxu_scale=1.66
>>
>> results: R=0.2294 R-free=0.2709 angl=1.087 bond=0.006
>>
>> 2) optimize_wxc = True  optimize_wxu = True wxc_scale=0.08 
>> wxu_scale=1.66
>>
>> results: R=0.2141 R-free=0.2628 angl=2.894 bond=0.033
>>
>> I am using the dev-412 version.  Thanks.
>>
>> -- Jianghai
>>
>>
>>
>>
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