Thanks for the reply. I think I didn't explain myself properly, of course I want to do bss, but we have noticed that previous versions of phenix (1.24 I think) did bss once per macro cycle and now with the newer versions, we get the same plus a final bbs cycle at the end of the whole process -shown in red- Is that final cycle introduced by default in the newer versions? Thanks again. Cesar. 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 On Dec 3, 2008, at 9:00 PM, [email protected] wrote:

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Today's Topics:

1. Bulk solvent ([email protected]) 2. Re: Bulk solvent (junfeng liu) 3. Re: Bulk solvent (Pavel Afonine) 4. Re: Bulk solvent (Pavel Afonine) 5. Re: Question regarding phenix.elbow (Nigel W Moriarty)

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Message: 1 Date: Wed, 3 Dec 2008 10:15:30 +0100 (CET) From: [email protected] Subject: [phenixbb] Bulk solvent To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain;charset=iso-8859-1

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 ---------------------------------------------------------------------- --

C?sar Santiago Dept of Macromolecules Structure Centro Nacional de Biotecnolog?a, CSIC Campus Cantoblanco 28049 Madrid Spain

[email protected]

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Message: 2 Date: Wed, 03 Dec 2008 09:36:30 +0000 From: junfeng liu Subject: Re: [phenixbb] Bulk solvent To: PHENIX user mailing list Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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 --------------------------------------------------------------------- ---

C?sar Santiago Dept of Macromolecules Structure Centro Nacional de Biotecnolog?a, CSIC Campus Cantoblanco 28049 Madrid Spain

[email protected]

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Message: 3 Date: Wed, 03 Dec 2008 08:09:57 -0800 From: Pavel Afonine Subject: Re: [phenixbb] Bulk solvent To: PHENIX user mailing list Cc: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi C?sar,

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 --------------------------------------------------------------------- ---

C?sar Santiago Dept of Macromolecules Structure Centro Nacional de Biotecnolog?a, CSIC Campus Cantoblanco 28049 Madrid Spain

[email protected]

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Message: 4 Date: Wed, 03 Dec 2008 08:13:21 -0800 From: Pavel Afonine Subject: Re: [phenixbb] Bulk solvent To: PHENIX user mailing list Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1"

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 -------------------------------------------------------------------- ----

C?sar Santiago Dept of Macromolecules Structure Centro Nacional de Biotecnolog?a, CSIC Campus Cantoblanco 28049 Madrid Spain

[email protected]

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