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 [email protected]
Add bulk_solvent_and_scale=False when you run it again. [email protected] 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
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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.
[email protected] 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
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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, [email protected] 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
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participants (3)
-
csantiag＠cnb.csic.es -
junfeng liu -
Pavel Afonine