[phenixbb] phenixbb Digest, Vol 37, Issue 3
CNB
csantiag at cnb.csic.es
Fri Dec 5 02:47:11 PST 2008
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, phenixbb-request at phenix-online.org wrote:
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> Today's Topics:
>
> 1. Bulk solvent (csantiag at cnb.csic.es)
> 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Dec 2008 10:15:30 +0100 (CET)
> From: csantiag at cnb.csic.es
> Subject: [phenixbb] Bulk solvent
> To: phenixbb at phenix-online.org
> Message-ID:
> <49732.150.244.83.180.1228295730.squirrel at webmail.cnb.csic.es>
> 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
>
> csantiag at cnb.csic.es
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 03 Dec 2008 09:36:30 +0000
> From: junfeng liu <jliu at nimr.mrc.ac.uk>
> Subject: Re: [phenixbb] Bulk solvent
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Message-ID: <4936531E.5030505 at nimr.mrc.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>> ---------------------------------------------------------------------
>> ---
>>
>>
>> C?sar Santiago
>> Dept of Macromolecules Structure
>> Centro Nacional de Biotecnolog?a, CSIC
>> Campus Cantoblanco
>> 28049 Madrid
>> Spain
>>
>> csantiag at cnb.csic.es
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 03 Dec 2008 08:09:57 -0800
> From: Pavel Afonine <pafonine at lbl.gov>
> Subject: Re: [phenixbb] Bulk solvent
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Cc: csantiag at cnb.csic.es
> Message-ID: <4936AF55.8010508 at lbl.gov>
> 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, 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
>> ---------------------------------------------------------------------
>> ---
>>
>>
>> C?sar Santiago
>> Dept of Macromolecules Structure
>> Centro Nacional de Biotecnolog?a, CSIC
>> Campus Cantoblanco
>> 28049 Madrid
>> Spain
>>
>> csantiag at cnb.csic.es
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 03 Dec 2008 08:13:21 -0800
> From: Pavel Afonine <pafonine at lbl.gov>
> Subject: Re: [phenixbb] Bulk solvent
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Message-ID: <4936B021.7010401 at lbl.gov>
> 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.
>>
>>
>>
>> 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
>>> --------------------------------------------------------------------
>>> ----
>>>
>>>
>>> C?sar Santiago
>>> Dept of Macromolecules Structure
>>> Centro Nacional de Biotecnolog?a, CSIC
>>> Campus Cantoblanco
>>> 28049 Madrid
>>> Spain
>>>
>>> csantiag at cnb.csic.es
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
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> ------------------------------
>
> Message: 5
> Date: Wed, 03 Dec 2008 11:32:05 -0800
> From: Nigel W Moriarty <NWMoriarty at lbl.gov>
> Subject: Re: [phenixbb] Question regarding phenix.elbow
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Message-ID: <4936DEB5.5030000 at lbl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> YoungJin
>
> I have fixed this error and its will be in the next release. Did you
> try ReadySet! as Pavel suggested? I can provide a restraints so
> you can
> continue your refinement if you desire.
>
> Thanks
>
> Nigel
>
> On 12/1/08 6:53 AM, Young-Jin Cho wrote:
>> Hi
>> I would like to know how I can add H atoms to my ligand, ADP in
>> the protein complex.
>> I was trying to add H atoms to one of my ligand, ADP.
>> When I types "phenix.elbow --final-
>> geometry=test10bcoot_h_refine_001.pdb --residue=ADP --
>> output=model_h",
>> it went on but failed with the following error message:
>> Traceback (most recent call last):
>> File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/
>> builder.py", line 1201, in <module>
>> run()
>> File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/
>> builder.py", line 1108, in run
>> molecule = post_process(molecule, options)
>> File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/
>> builder.py", line 577, in post_process
>> options,
>> File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/
>> optimisation_manager.py", line 331, in optimisation_manager
>> pre_opt))
>> File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/
>> IOMixins.py", line 857, in WritePDB
>> original_order=original_order,
>> File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/
>> IOMixins.py", line 965, in WritePDB2String
>> self.AdjustHydrogenNames()
>> File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/
>> IOMixins.py", line 940, in AdjustHydrogenNames
>> if test_name[3]==" ": test_name[3]="0"
>> TypeError: 'str' object does not support item assignment
>>
>> FYI. ADP is names as ADP as a residue name in the pdb file but has
>> different chain names.
>>
>> By the way, I should mention that I used phenix.reduce first for
>> adding H atoms but it was not able to add sugar H's in ADP
>> molecule albeit other residues were fine.
>>
>> Thanks in advance for your help.
>>
>> Best,
>> YoungJin
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
> --
> Nigel W. Moriarty
> Building 64R0246B, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709
> Fax : 510-486-5909
> Email : NWMoriarty at LBL.gov
> Web : CCI.LBL.gov
>
>
>
> ------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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>
> End of phenixbb Digest, Vol 37, Issue 3
> ***************************************
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