[phenixbb] Bulk solvent
Pavel Afonine
pafonine at lbl.gov
Wed Dec 3 08:13:21 PST 2008
Yes, this will turn bulk solvent correction and anisotropic scaling off
completely. In some cases it may result in R-factors increase by ~5% or
similar. So it may only make sense in exotic cases or if you do
numerical experiments (simulated data etc..).
Pavel.
On 12/3/2008 1:36 AM, junfeng liu wrote:
> Add
>
> bulk_solvent_and_scale=False
> when you run it again.
>
>
>
> csantiag at cnb.csic.es wrote:
>
>> Hi all,
>> I'm refining a protein and after running phenix.refine I always get a bulk
>> solvent refinement cycle at the end of the process. Is there any way to
>> get rid of the last step?
>>
>> ------------------------------------------------------------------------
>> REMARK stage angl bond chir dihe plan repu geom_target
>> REMARK 0 : 1.007 0.027 0.237 18.975 0.004 4.107 2.7953e-01
>> REMARK 1_bss: 1.007 0.027 0.237 18.975 0.004 4.107 2.7953e-01
>> REMARK 1_xyz: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01
>> REMARK 1_adp: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01
>> REMARK 2_bss: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01
>> REMARK 2_xyz: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01
>> REMARK 2_adp: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01
>> REMARK 3_bss: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01
>> REMARK 3_xyz: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01
>> REMARK 3_adp: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01
>> REMARK 3_bss: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01
>> REMARK
>> ------------------------------------------------------------------------
>>
>>
>> César Santiago
>> Dept of Macromolecules Structure
>> Centro Nacional de Biotecnología, CSIC
>> Campus Cantoblanco
>> 28049 Madrid
>> Spain
>>
>> csantiag at cnb.csic.es
>>
>>
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>>
>>
>>
>
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