[phenixbb] Bulk solvent

[Pavel Afonine]

Hi César,

this step is important. Bulk solvent modeling is based on mask 
calculation and since during refinement of coordinates the atoms shift 
the mask gets invalidated. This is why we do a final bulk solvent 
correction step at the very last step of refinement just before the 
final statistics is reported. So I'm puzzled about why you want to turn 
it off. If it causes any problem, it's much better to find out the 
primary reason for it rather than turn bulk solvent correction. Could 
you please give more details?

If you do "main.bulk_solvent_and_scale=false" phenix.refine will not do 
bulk solvent correction and anisotropic scaling at all which is bad.

Pavel.

On 12/3/2008 1:15 AM, 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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