[phenixbb] phenix.development.optimize_model

Colin Levy C.Levy at manchester.ac.uk
Wed Mar 18 08:51:28 PDT 2015


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:

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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
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>------------------------------
>
>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
>
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>------------------------------
>
>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
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>------------------------------
>
>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
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>------------------------------
>
>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
>
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>
>------------------------------
>
>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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