[phenixbb] phenix.development.optimize_model
Pavel Afonine
pafonine at lbl.gov
Wed Mar 18 18:17:30 PDT 2015
Hi Colin,
I don't know what phenix.development.optimize_model is. Perhaps one of
developers added it for testing/development purposes not for end-users.
I suggest you use phenix.refine in the GUI or command line, which is
well tested both by time and extensive sets of tests.
You cannot combine TLS and individual anisotropic ADP refinement, so
regardless what tool you used it's either TLS or individual anisotropic
ADP refinement, not both.
Pavel
On 3/18/15 8:51 AM, Colin Levy wrote:
> Hi,
>
> I am running a Phenix development installation (dev_1977) and used the
> phenix.development.optimize_model option on a project of mine refined at
> 1.9Å. The output has certainly improved the R factors but I was curious as
> the refined model which is a rather globular structure has been refined
> utilising 17 TLS groups and anisotropic B factors. In its current state of
> development, how robust are these refinement choices and on what basis are
> they being determined? They differ somewhat from what I might have invoked
> manually?
>
> Many thanks,
>
> Colin
>
>
>
>
> Manchester
> Protein
> Structure
> Facility
>
> Dr. Colin W. Levy
> MIB G034
> Tel. 0161 275 5090
> Mob.07786 197 554
> c.levy at manchester.ac.uk
>
>
>
>
>
>
>
>
> On 12/03/2015 15:19, "phenixbb-request at phenix-online.org"
> <phenixbb-request at phenix-online.org> wrote:
>
>> Send phenixbb mailing list submissions to
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>>
>> Today's Topics:
>>
>> 1. Announcement and call for abstracts: Structural
>> Bioinformatics microsymposium at ECM29, August 23-28, Rovinj,
>> Croatia (Capitani Guido (PSI))
>> 2. how to correct residuess with missing atoms (Smith Liu)
>> 3. Re: how to correct residuess with missing atoms (Joel Tyndall)
>> 4. RESOLVE density modification (Mark A Saper)
>> 5. Re: RESOLVE density modification (Terwilliger, Thomas Charles)
>> 6. Nitric Oxide metal.edits not working? (Yarrow Madrona)
>> 7. Re: Nitric Oxide metal.edits not working? (Edward A. Berry)
>> 8. Group B factor refinement not working for low resolution data (??)
>> 9. Re: Group B factor refinement not working for low resolution
>> data (Pavel Afonine)
>> 10. Re: Group B factor refinement not working for low resolution
>> data (Phoebe A. Rice)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 6 Mar 2015 13:29:51 +0000
>> From: "Capitani Guido (PSI)" <guido.capitani at psi.ch>
>> To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
>> Subject: [phenixbb] Announcement and call for abstracts: Structural
>> Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, Croatia
>> Message-ID:
>> <D324C9581FD3114280044EDC6357A3E51BCE66CD at MBX114.d.ethz.ch>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Dear Colleagues,
>>
>> The 29th European Crystallographic Meeting (ECM29), to be held on August
>> 23-28 in Rovinj, Croatia, will feature a Structural Bioinformatics
>> microsymposium
>> (http://ecm29.ecanews.org/programme/microsymposia/#ms10). All structural
>> bioinformatics topics with relevance to macromolecular crystallography
>> are welcome.
>> Abstract submission (for oral or poster presentation) is available at
>> http://ecm29.ecanews.org/participate/abstract-submission/, with deadline
>> March 23.
>> The final program will encompass two 30-min talks from invited speakers,
>> three 20-min talks chosen from the submitted abstracts, and poster
>> presentations.
>> Looking forward to many interesting contributions; with best regards,
>>
>> Guido Capitani
>>
>>
>>
>> Dr. Guido Capitani
>> Paul Scherrer Institute
>> OFLC/110
>> 5232 Villigen PSI
>> Switzerland
>> guido.capitani at psi.ch
>> Tel. +41 56 310 47 22
>> http://www.psi.ch/lbr/capitani_-guido
>> http://www.eppic-web.org
>>
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Sun, 8 Mar 2015 18:11:19 +0800 (CST)
>> From: "Smith Liu" <smith_liu123 at 163.com>
>> To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
>> Subject: [phenixbb] how to correct residuess with missing atoms
>> Message-ID: <46870f8b.b136.14bf8de1901.Coremail.smith_liu123 at 163.com>
>> Content-Type: text/plain; charset="gbk"
>>
>> Dear All,
>>
>> Is any function of Phenix or some other software which can be used to
>> correct residuess with missing atoms in the PDB file?
>>
>> I am looking forward to getting your reply.
>>
>> Smith
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
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>> /attachment-0001.htm>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Sun, 8 Mar 2015 20:51:18 +0000
>> From: Joel Tyndall <joel.tyndall at otago.ac.nz>
>> To: Smith Liu <smith_liu123 at 163.com>, "phenixbb at phenix-online.org"
>> <phenixbb at phenix-online.org>
>> Subject: Re: [phenixbb] how to correct residuess with missing atoms
>> Message-ID:
>> <0DDD35E86921D947AFE9571F16DA7D6B2F6584A5 at ITS-EXM-P05.registry.otago.ac.n
>> z>
>>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Dear Smith,
>>
>> You can use the mutate function in either Coot or pymol. I am not aware
>> of how or if this can be done in Phenix
>>
>> Hope this helps
>>
>> Joel
>>
>> From: phenixbb-bounces at phenix-online.org
>> [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Smith Liu
>> Sent: Sunday, 8 March 2015 11:11 p.m.
>> To: phenixbb at phenix-online.org
>> Subject: [phenixbb] how to correct residuess with missing atoms
>>
>> Dear All,
>>
>> Is any function of Phenix or some other software which can be used to
>> correct residuess with missing atoms in the PDB file?
>>
>> I am looking forward to getting your reply.
>>
>> Smith
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://phenix-online.org/pipermail/phenixbb/attachments/20150308/540f042c
>> /attachment-0001.htm>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Sun, 8 Mar 2015 22:15:53 -0400
>> From: Mark A Saper <saper at umich.edu>
>> To: phenixbb at phenix-online.org
>> Subject: [phenixbb] RESOLVE density modification
>> Message-ID: <769A57B6-615E-4736-8C24-A093163DCC36 at umich.edu>
>> Content-Type: text/plain; charset=windows-1252
>>
>> I am trying to run RESOLVE density modification with the output of a SAD
>> Phaser run (dev-1965). There are 3 input files: high
>> resolution/experimental F?s and I?s, map coefficients and phases, and
>> sequence.
>> I consistently get this error:
>> ?
>> **************************************************************************
>> ******
>> Failed to carry out AutoBuild_set_up_build:
>>
>> For finding NCS from sites an MTZ file is required
>> **************************************************************************
>> ******
>>
>> I do not know which MTZ file is being referred to. I have tried entering
>> NCS as blank, 1, or turning it off in the NCS? options panel. I also
>> tried including the substructure PDB file. Any suggestions?
>>
>> -Mark
>> _________________________________
>> Mark A. Saper, Ph.D.
>> Associate Professor of Biological Chemistry, University of Michigan
>> Ann Arbor MI 48109-1055 U.S.A.
>> saper at umich.edu phone (734) 764-3353 fax (734) 764-3323
>>
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Mon, 9 Mar 2015 15:18:15 +0000
>> From: "Terwilliger, Thomas Charles" <terwilliger at lanl.gov>
>> To: Mark A Saper <saper at umich.edu>, "phenixbb at phenix-online.org"
>> <phenixbb at phenix-online.org>
>> Subject: Re: [phenixbb] RESOLVE density modification
>> Message-ID:
>> <AD56E2411D1DF44889DF34878BB330795B7B19AB at ECS-EXG-P-MB01.win.lanl.gov>
>> Content-Type: text/plain; charset="Windows-1252"
>>
>> Hi Mark,
>> I'm sorry, this must be a bug in the program. If you are running a
>> recent version, can you possibly send me the input files and the full log
>> file and I'll fix it?
>> Thanks a lot!
>> -Tom T
>>
>> ________________________________________
>> From: phenixbb-bounces at phenix-online.org
>> [phenixbb-bounces at phenix-online.org] on behalf of Mark A Saper
>> [saper at umich.edu]
>> Sent: Sunday, March 08, 2015 8:15 PM
>> To: phenixbb at phenix-online.org
>> Subject: [phenixbb] RESOLVE density modification
>>
>> I am trying to run RESOLVE density modification with the output of a SAD
>> Phaser run (dev-1965). There are 3 input files: high
>> resolution/experimental F?s and I?s, map coefficients and phases, and
>> sequence.
>> I consistently get this error:
>> ?
>> **************************************************************************
>> ******
>> Failed to carry out AutoBuild_set_up_build:
>>
>> For finding NCS from sites an MTZ file is required
>> **************************************************************************
>> ******
>>
>> I do not know which MTZ file is being referred to. I have tried entering
>> NCS as blank, 1, or turning it off in the NCS? options panel. I also
>> tried including the substructure PDB file. Any suggestions?
>>
>> -Mark
>> _________________________________
>> Mark A. Saper, Ph.D.
>> Associate Professor of Biological Chemistry, University of Michigan
>> Ann Arbor MI 48109-1055 U.S.A.
>> saper at umich.edu phone (734) 764-3353 fax (734) 764-3323
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Mon, 9 Mar 2015 16:49:32 -0700
>> From: Yarrow Madrona <amadrona at uci.edu>
>> To: PHENIX user mailing list <phenixbb at phenix-online.org>
>> Subject: [phenixbb] Nitric Oxide metal.edits not working?
>> Message-ID:
>> <CAMHjG6b_fnxz4M9LZtZY-NHurfmajMZTzsSshfpKqKm-aNQpCw at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hello,
>>
>> I am running phenix version 1.9-1692. I have restrains for a nitric oxide
>> ligand that I have used previously to refine a heme iron-NO linked
>> structure. I have pasted them below. For some reason. The NO always gets
>> moved a little to far from the iron. Here is a coot screen shot:
>>
>> https://www.dropbox.com/s/85c1ad2kecwebij/coot.png?dl=0
>> Can someone please help me resolve this issue? Thank you.
>>
>> -Yarrow
>>
>> --------------------------------------------------------------------------
>> --------
>> metal edits file:
>>
>> refinement.geometry_restraints.edits {
>> bond {
>> action = *add
>> atom_selection_1 = name FE and chain A and resname FE and resseq
>> 499
>> atom_selection_2 = name N and chain A and resname NMO and resseq
>> 510
>> distance_ideal = 1.75
>> sigma = 0.1
>> }
>> }
>>
>> refinement.geometry_restraints.edits {
>> angle {
>> action = *add
>> atom_selection_1 = name FE and chain A and resname FE and resseq 499
>> atom_selection_2 = name N and chain A and resname NMO and resseq
>> 510
>> atom_selection_3 = name O and chain A and resname NMO and resseq
>> 510
>> angle_ideal = 160
>> sigma = 5
>> }
>> }
>>
>> refinement.geometry_restraints.edits {
>> bond {
>> action = *add
>> atom_selection_1 = name FE and chain B and resname FE and resseq
>> 499
>> atom_selection_2 = name N and chain B and resname NMO and resseq
>> 510
>> distance_ideal = 1.75
>> sigma = 0.1
>> }
>> }
>>
>> refinement.geometry_restraints.edits {
>> angle {
>> action = *add
>> atom_selection_1 = name FE and chain B and resname FE and resseq
>> 499
>> atom_selection_2 = name N and chain B and resname NMO and resseq
>> 510
>> atom_selection_3 = name O and chain B and resname NMO and resseq
>> 510
>> angle_ideal = 160
>> sigma = 5
>> }
>> }
>> ---------------------------------------------------------------------
>> CIF file
>>
>> #
>> data_comp_list
>> loop_
>> _chem_comp.id
>> _chem_comp.three_letter_code
>> _chem_comp.name
>> _chem_comp.group
>> _chem_comp.number_atoms_all
>> _chem_comp.number_atoms_nh
>> _chem_comp.desc_level
>> NMO NMO "nitric oxide " ligand 2 2 .
>> #
>> data_comp_NMO
>> #
>> loop_
>> _chem_comp_atom.comp_id
>> _chem_comp_atom.atom_id
>> _chem_comp_atom.type_symbol
>> _chem_comp_atom.type_energy
>> _chem_comp_atom.partial_charge
>> _chem_comp_atom.x
>> _chem_comp_atom.y
>> _chem_comp_atom.z
>> NMO N N N . -0.1324 -0.0924 0.5896
>> NMO O O O . 0.1324 0.0924 -0.5896
>> #
>> loop_
>> _chem_comp_bond.comp_id
>> _chem_comp_bond.atom_id_1
>> _chem_comp_bond.atom_id_2
>> _chem_comp_bond.type
>> _chem_comp_bond.value_dist
>> _chem_comp_bond.value_dist_esd
>> NMO N O double 1.223 0.020
>> #
>> loop_
>> _chem_comp_plane_atom.comp_id
>> _chem_comp_plane_atom.plane_id
>> _chem_comp_plane_atom.atom_id
>> _chem_comp_plane_atom.dist_esd
>> NMO plan-1 N 0.020
>> NMO plan-1 O 0.020
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://phenix-online.org/pipermail/phenixbb/attachments/20150309/1278a43e
>> /attachment-0001.htm>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Mon, 09 Mar 2015 22:17:08 -0400
>> From: "Edward A. Berry" <BerryE at upstate.edu>
>> To: Yarrow Madrona <amadrona at uci.edu>, PHENIX user mailing list
>> <phenixbb at phenix-online.org>
>> Subject: Re: [phenixbb] Nitric Oxide metal.edits not working?
>> Message-ID: <54FE5424.3070908 at upstate.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Are you sure the resname of the heme iron is FE? Usually heme Fe is one
>> atom of the HEM residue, like
>> atom_selection_1 = name FE and chain A and resname HEM and resseq
>> 499
>> (But if that were the problem I think phenix.refine ^^^
>> would stop and tell you)
>>
>> On 03/09/2015 07:49 PM, Yarrow Madrona wrote:
>>> Hello,
>>>
>>> I am running phenix version 1.9-1692. I have restrains for a nitric
>>> oxide ligand that I have used previously to refine a heme iron-NO linked
>>> structure. I have pasted them below. For some reason. The NO always gets
>>> moved a little to far from the iron. Here is a coot screen shot:
>>>
>>> https://www.dropbox.com/s/85c1ad2kecwebij/coot.png?dl=0
>>> Can someone please help me resolve this issue? Thank you.
>>>
>>> -Yarrow
>>>
>>>
>>> -------------------------------------------------------------------------
>>> ---------
>>> metal edits file:
>>>
>>> refinement.geometry_restraints.edits {
>>> bond {
>>> action = *add
>>> atom_selection_1 = name FE and chain A and resname FE and resseq
>>> 499
>>> atom_selection_2 = name N and chain A and resname NMO and
>>> resseq 510
>>> distance_ideal = 1.75
>>> sigma = 0.1
>>> }
>>> }
>>>
>>> refinement.geometry_restraints.edits {
>>> angle {
>>> action = *add
>>> atom_selection_1 = name FE and chain A and resname FE and resseq
>>> 499
>>> atom_selection_2 = name N and chain A and resname NMO and
>>> resseq 510
>>> atom_selection_3 = name O and chain A and resname NMO and
>>> resseq 510
>>> angle_ideal = 160
>>> sigma = 5
>>> }
>>> }
>>>
>>> refinement.geometry_restraints.edits {
>>> bond {
>>> action = *add
>>> atom_selection_1 = name FE and chain B and resname FE and resseq
>>> 499
>>> atom_selection_2 = name N and chain B and resname NMO and
>>> resseq 510
>>> distance_ideal = 1.75
>>> sigma = 0.1
>>> }
>>> }
>>>
>>> refinement.geometry_restraints.edits {
>>> angle {
>>> action = *add
>>> atom_selection_1 = name FE and chain B and resname FE and resseq
>>> 499
>>> atom_selection_2 = name N and chain B and resname NMO and
>>> resseq 510
>>> atom_selection_3 = name O and chain B and resname NMO and
>>> resseq 510
>>> angle_ideal = 160
>>> sigma = 5
>>> }
>>> }
>>> ---------------------------------------------------------------------
>>> CIF file
>>>
>>> #
>>> data_comp_list
>>> loop_
>>> _chem_comp.id <http://chem_comp.id/>
>>> _chem_comp.three_letter_code
>>> _chem_comp.name <http://chem_comp.name/>
>>> _chem_comp.group
>>> _chem_comp.number_atoms_all
>>> _chem_comp.number_atoms_nh
>>> _chem_comp.desc_level
>>> NMO NMO "nitric oxide " ligand 2 2 .
>>> #
>>> data_comp_NMO
>>> #
>>> loop_
>>> _chem_comp_atom.comp_id
>>> _chem_comp_atom.atom_id
>>> _chem_comp_atom.type_symbol
>>> _chem_comp_atom.type_energy
>>> _chem_comp_atom.partial_charge
>>> _chem_comp_atom.x
>>> _chem_comp_atom.y
>>> _chem_comp_atom.z
>>> NMO N N N . -0.1324 -0.0924 0.5896
>>> NMO O O O . 0.1324 0.0924 -0.5896
>>> #
>>> loop_
>>> _chem_comp_bond.comp_id
>>> _chem_comp_bond.atom_id_1
>>> _chem_comp_bond.atom_id_2
>>> _chem_comp_bond.type
>>> _chem_comp_bond.value_dist
>>> _chem_comp_bond.value_dist_esd
>>> NMO N O double 1.223 0.020
>>> #
>>> loop_
>>> _chem_comp_plane_atom.comp_id
>>> _chem_comp_plane_atom.plane_id
>>> _chem_comp_plane_atom.atom_id
>>> _chem_comp_plane_atom.dist_esd
>>> NMO plan-1 N 0.020
>>> NMO plan-1 O 0.020
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Wed, 11 Mar 2015 22:30:33 -0400
>> From: ?? <lixiang1642 at gmail.com>
>> To: PHENIX user mailing list <phenixbb at phenix-online.org>
>> Subject: [phenixbb] Group B factor refinement not working for low
>> resolution data
>> Message-ID:
>> <CAE5L1v_xxmLSJzn6-TzqmFP=dL53wDjqyTTb51asQmEGhNTebw at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi,
>>
>> I am working on my ~6A data with molecular replacement method. The MR
>> works
>> out and after rigid body and xyz refinement the result is OK. However,
>> when
>> I tried the ADP refinement with Group B factor option in PHENIX GUI, the R
>> factor significantly increased as well as the B-factor. Any expert can
>> help
>> me to take a look and give some suggestions please?
>>
>> Thank you very much for your help!
>>
>> Sincerely,
>> Xiang
>>
>> --
>> Li Xiang
>> Department of chemistry,
>> University of Michigan
>> Email?lixiang1642 at gmail.com
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://phenix-online.org/pipermail/phenixbb/attachments/20150311/da98fc8b
>> /attachment-0001.htm>
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Wed, 11 Mar 2015 22:35:38 -0700
>> From: Pavel Afonine <pafonine at lbl.gov>
>> To: ?? <lixiang1642 at gmail.com>, PHENIX user mailing list
>> <phenixbb at phenix-online.org>
>> Subject: Re: [phenixbb] Group B factor refinement not working for low
>> resolution data
>> Message-ID: <550125AA.7070201 at lbl.gov>
>> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>>
>> Hello Xiang,
>>
>> short answer: try refining with all defaults plus weight optimization.
>> If that does not go well please send me data and model files and I will
>> do my best to make it work.
>>
>> Longer answer: the way B-factor restraints are implemented in
>> phenix.refine (that you can learn about in corresponding paper) allows
>> refining individual Bs at any resolution. So this is why this is the
>> first choice to try. If that does not work it's best to a) let us know
>> and b) try group B refinement.
>>
>> Pavel
>>
>> On 3/11/15 7:30 PM, ?? wrote:
>>> Hi,
>>>
>>> I am working on my ~6A data with molecular replacement method. The MR
>>> works out and after rigid body and xyz refinement the result is OK.
>>> However, when I tried the ADP refinement with Group B factor option in
>>> PHENIX GUI, the R factor significantly increased as well as the
>>> B-factor. Any expert can help me to take a look and give some
>>> suggestions please?
>>>
>>> Thank you very much for your help!
>>>
>>> Sincerely,
>>> Xiang
>>>
>>> --
>>> Li Xiang
>>> Department of chemistry,
>>> University of Michigan
>>> Email?lixiang1642 at gmail.com <mailto:lixiang1642 at gmail.com>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://phenix-online.org/pipermail/phenixbb/attachments/20150311/e88ccf63
>> /attachment-0001.htm>
>>
>> ------------------------------
>>
>> Message: 10
>> Date: Thu, 12 Mar 2015 15:18:48 +0000
>> From: "Phoebe A. Rice" <price at uchicago.edu>
>> To: Pavel Afonine <pafonine at lbl.gov>, ?? <lixiang1642 at gmail.com>,
>> PHENIX user mailing list <phenixbb at phenix-online.org>
>> Subject: Re: [phenixbb] Group B factor refinement not working for low
>> resolution data
>> Message-ID:
>> <089821C8F2223D4DBFC0B8B4B224C6733796F24F at xm-mbx-08-prod.ad.uchicago.edu>
>>
>> Content-Type: text/plain; charset="iso-2022-jp"
>>
>> I've been refining a 3.4A structure (now using dev-1951) and find that
>> anything besides TLS (with multiple groups at least) makes Rs go up. A
>> lot. And I am asking it to optimize weights.
>>
>>
>> ++++++++++++++++++++++++++++++++++++++++++
>>
>> Phoebe A. Rice
>> Dept. of Biochemistry & Molecular Biology
>> The University of Chicago
>>
>> PRice at uchicago.edu<mailto:PRice at uchicago.edu>
>> ________________________________
>> From: phenixbb-bounces at phenix-online.org
>> [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine
>> [pafonine at lbl.gov]
>> Sent: Thursday, March 12, 2015 12:35 AM
>> To: ??; PHENIX user mailing list
>> Subject: Re: [phenixbb] Group B factor refinement not working for low
>> resolution data
>>
>> Hello Xiang,
>>
>> short answer: try refining with all defaults plus weight optimization. If
>> that does not go well please send me data and model files and I will do
>> my best to make it work.
>>
>> Longer answer: the way B-factor restraints are implemented in
>> phenix.refine (that you can learn about in corresponding paper) allows
>> refining individual Bs at any resolution. So this is why this is the
>> first choice to try. If that does not work it's best to a) let us know
>> and b) try group B refinement.
>>
>> Pavel
>>
>> On 3/11/15 7:30 PM, ?? wrote:
>> Hi,
>>
>> I am working on my ~6A data with molecular replacement method. The MR
>> works out and after rigid body and xyz refinement the result is OK.
>> However, when I tried the ADP refinement with Group B factor option in
>> PHENIX GUI, the R factor significantly increased as well as the B-factor.
>> Any expert can help me to take a look and give some suggestions please?
>>
>> Thank you very much for your help!
>>
>> Sincerely,
>> Xiang
>>
>> --
>> Li Xiang
>> Department of chemistry,
>> University of Michigan
>> Email?lixiang1642 at gmail.com<mailto:lixiang1642 at gmail.com>
>>
>>
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