[phenixbb] Map after refinement
Xuewu Zhang
xuewu.zhang at gmail.com
Fri Feb 26 19:54:31 PST 2010
To Paul,
No, I used the mtz format map file in coot.
TO Pavel,
I will send you the files tomorrow. The command I used is the simplest one:
phenix.refine input.pdb input.mtz.
By the way, the same thing happened to one of my colleagues here a while
ago. She solved the problem by updating to the then new 1.5 version.
Thanks you guys for the quick replies.
Xuewu Zhang
UT Southwestern Medical Center
On Fri, Feb 26, 2010 at 4:29 PM, <phenixbb-request at phenix-online.org> wrote:
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> Today's Topics:
>
> 1. Int'l Workshop on Macromolecular Crystallography - South
> America (Alejandro Buschiazzo)
> 2. Re: Gap between R and Rfree (Felix Frolow)
> 3. Re: Map after refinement (Xuewu Zhang)
> 4. Re: Map after refinement (Paul Adams)
> 5. Re: Map after refinement (Pavel Afonine)
> 6. weaker density in maps (David Garboczi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 26 Feb 2010 18:17:06 -0200
> From: Alejandro Buschiazzo <alebus at pasteur.edu.uy>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: [phenixbb] Int'l Workshop on Macromolecular Crystallography -
> South America
> Message-ID: <4B882C42.9080701 at pasteur.edu.uy>
> Content-Type: text/plain; charset=windows-1252; format=flowed
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> Dear colleagues,
>
> just a reminder, we're close to the deadline for applications. Details
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>
> -----------------------------------------------------------------------------------------------------------------------
>
> *International Workshop ?Macromolecular Crystallography : Introduction
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>
> All applications should be received until March 7 2010. They should be
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>
> *ORGANIZERS*
>
> Dr. Alejandro Buschiazzo
> Unidad de Cristalograf?a de Prote?nas
> Institut Pasteur de Montevideo
>
> Dr. Pedro Alzari
> Departamento de Biolog?a Estructural y Qu?mica
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> ------------------------------
>
> Message: 2
> Date: Fri, 26 Feb 2010 22:18:33 +0200
> From: Felix Frolow <mbfrolow at post.tau.ac.il>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Gap between R and Rfree
> Message-ID: <F52C4FE8-AE34-4C23-B74E-A923995E5831 at post.tau.ac.il>
> Content-Type: text/plain; charset=us-ascii
>
> Yea Phil, You have got them
> I was accused several years ago for over-fitting Rfree !!!!!!!
> The bad thing is that to publish you have to avoid arguing with these
> post-crystallography era referees.
> Today they ask meaningless question " I am novice to crystallography, teach
> me how to minimize Rfree"
> Tomorrow they referee you papers and make meaningless remarks about gap
> between R and Rfree
> " Your R factor is 17% and Rfree is 24%, it rase question"
> geeeeek!!!!!! what question?????
> Dr Felix Frolow
> Professor of Structural Biology and Biotechnology
> Department of Molecular Microbiology
> and Biotechnology
> Tel Aviv University 69978, Israel
>
> Acta Crystallographica D, co-editor
>
> e-mail: mbfrolow at post.tau.ac.il
> Tel: ++972 3640 8723
> Fax: ++972 3640 9407
> Cellular: ++972 547 459 608
>
> On Feb 26, 2010, at 11:30 , Phil Evans wrote:
>
> >
> > I do worry a bit about the fetishisation of R-factors, to the point where
> I get the impression that some people think that the object of refinement is
> minimisation of Rfree. The aim is to produce the "best" model consistent
> with the data, and the most important tool is looking at the maps on the
> graphics, in conjunction with validation tools analysing consistency with
> what we know about stereochemistry (Ramachandran, rotamers, bumps etc). Also
> is your model consistent with your initial experimental phased map, if
> available? The Rfree is a useful guide, but no more than that.
> >
> > My (admittedly superficial) experience of changing weights, freeR
> selection, resolution limits, NCS, etc in refinement is that often you can
> spend some time doing this, maybe improve the R-factors a bit, but end up
> with a model which is indistinguishable from the previous model when
> superimposed on it.
> >
> > I'm fed up with referees telling me my structure must be wrong because
> the Rfree is "too high" (and I haven't followed their particular pet
> protocol), when I know that it is essentially correct, and as good as I can
> make it.
> >
> > Phil
> >
> >
> > On 26 Feb 2010, at 01:49, Pavel Afonine wrote:
> >
> >> Hi Simon,
> >>
> >> the next available PHENIX nightly build will have this command:
> >>
> >> phenix.r_factor_statistics
> >>
> >> This will output a plain text histograms for Rwork, Rfree and
> Rfree-Rwork. For example:
> >>
> >> ***
> >> phenix.r_factor_statistics 2.5 left_offset=0.2 right_offset=0.2 n_bins=5
> >> Command used:
> >>
> >> phenix.r_factor_statistics 2.500 left_offset=0.200 right_offset=0.200
> n_bins=5
> >>
> >>
> >> Histogram of Rwork for models in PDB at resolution 2.30-2.70 A:
> >> 0.115 - 0.168 : 149
> >> 0.168 - 0.220 : 2998
> >> 0.220 - 0.273 : 1879
> >> 0.273 - 0.325 : 67
> >> 0.325 - 0.378 : 2
> >> Histogram of Rfree for models in PDB at resolution 2.30-2.70 A:
> >> 0.146 - 0.210 : 116
> >> 0.210 - 0.274 : 3288
> >> 0.274 - 0.337 : 1664
> >> 0.337 - 0.401 : 26
> >> 0.401 - 0.465 : 1
> >> Histogram of Rfree-Rwork for all model in PDB at resolution 2.30-2.70 A:
> >> 0.001 - 0.021 : 233
> >> 0.021 - 0.041 : 1412
> >> 0.041 - 0.060 : 2180
> >> 0.060 - 0.080 : 1045
> >> 0.080 - 0.100 : 225
> >> Number of structures considered: 5095
> >> ***
> >>
> >> and running it without arguments will take all structures.
> >>
> >> Pavel.
> >>
> >>
> >>
> >> On 2/25/10 2:01 PM, Simon Kolstoe wrote:
> >>> oh yes please Pavel (command line polygon/statistics overview) - could
> the output be a pdf or ps rather than just starting up the GUI?
> >>>
> >>> Simon
> >>>
> >>>
> >>>
> >>> On 25 Feb 2010, at 19:39, Pavel Afonine wrote:
> >>>
> >>>> Hi Francis,
> >>>>
> >>>> in PHENIX GUI: "Validation" -> "PDB Statistics Overview"
> >>>>
> >>>> or:
> >>>>
> >>>> in PHENIX GUI: "Validation" -> "POLYGON"
> >>>>
> >>>> The underlying idea is published here:
> >>>>
> >>>> Crystallographic model quality at a glance. L. Urzhumtseva, P. V.
> Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009)
> >>>>
> >>>> I can add a command line version if anyone is interested.
> >>>>
> >>>> Pavel.
> >>>>
> >>>>
> >>>>
> >>>> On 2/25/10 9:45 AM, Francis E Reyes wrote:
> >>>>> Pavel
> >>>>>
> >>>>> What phenix utility produces such information?
> >>>>> Thx
> >>>>>
> >>>>> FR
> >>>>>
> >>>>> On Feb 25, 2010, at 10:43 AM, Pavel Afonine <PAfonine at lbl.gov>
> wrote:
> >>>>>
> >>>>>> Hi Young-Jin,
> >>>>>>
> >>>>>> the distribution of R-factors for all structures in PDB refined at
> resolutions between 2.4 and 2.6 A is following:
> >>>>>>
> >>>>>> Histogram of Rwork for all model in PDB at resolution 2.40-2.60:
> >>>>>> 0.115 - 0.141 : 5
> >>>>>> 0.141 - 0.168 : 69
> >>>>>> 0.168 - 0.194 : 414
> >>>>>> 0.194 - 0.220 : 955 <<<<< your structure
> >>>>>> 0.220 - 0.246 : 695
> >>>>>> 0.246 - 0.273 : 153
> >>>>>> 0.273 - 0.299 : 25
> >>>>>> 0.299 - 0.325 : 5
> >>>>>> 0.325 - 0.352 : 0
> >>>>>> 0.352 - 0.378 : 1
> >>>>>> Histogram of Rfree for all model in PDB at resolution 2.40-2.60:
> >>>>>> 0.146 - 0.178 : 3
> >>>>>> 0.178 - 0.210 : 41
> >>>>>> 0.210 - 0.242 : 404
> >>>>>> 0.242 - 0.274 : 1104
> >>>>>> 0.274 - 0.305 : 653 <<<<< your structure
> >>>>>> 0.305 - 0.337 : 108
> >>>>>> 0.337 - 0.369 : 8
> >>>>>> 0.369 - 0.401 : 0
> >>>>>> 0.401 - 0.433 : 0
> >>>>>> 0.433 - 0.465 : 1
> >>>>>> Histogram of Rfree-Rwork for all model in PDB at resolution
> 2.40-2.60:
> >>>>>> 0.002 - 0.012 : 28
> >>>>>> 0.012 - 0.022 : 83
> >>>>>> 0.022 - 0.031 : 232
> >>>>>> 0.031 - 0.041 : 430
> >>>>>> 0.041 - 0.051 : 458
> >>>>>> 0.051 - 0.061 : 493
> >>>>>> 0.061 - 0.071 : 298
> >>>>>> 0.071 - 0.080 : 186
> >>>>>> 0.080 - 0.090 : 85 <<<<< your structure
> >>>>>> 0.090 - 0.100 : 29
> >>>>>>
> >>>>>> which I interpret as your Rwork is most likely good as well as
> Rfree, but the gap Rfree-Rwork is too large meaning possible overfitting.
> >>>>>>
> >>>>>> A few tips:
> >>>>>> - if you have NCS - use it in refinement;
> >>>>>> - optimize refinement target weights: a) automatically:
> "optimize_wxc=true optimize_wxu=true", or b) manually using wxc_scale and
> wxu_scale parameters;
> >>>>>> - make sure you use the latest PHENIX version.
> >>>>>>
> >>>>>> Let me now if you have any questions.
> >>>>>>
> >>>>>> Pavel.
> >>>>>>
> >>>>>>
> >>>>>> On 2/25/10 9:17 AM, Young-Jin Cho wrote:
> >>>>>>> Hi everyone,
> >>>>>>> I recently got a diffraction data and am trying to refine it. The
> question is whatever I did the gap between R and Rfree stay far away:
> .2140/.2982 around 2.5 A resolution. (water added and
> isotropic(individual_adp) and so on).
> >>>>>>> Although I am redoing with many different approaches, if anyone can
> give me any comments or suggestions, it would be helpful.
> >>>>>>>
> >>>>>>> Thanks in advance,
> >>>>>>>
> >>>>>>> Young-Jin
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> phenixbb mailing list
> >>>>>>> phenixbb at phenix-online.org
> >>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
> >>>>>>>
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>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 26 Feb 2010 14:31:26 -0600
> From: Xuewu Zhang <xuewu.zhang at gmail.com>
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Map after refinement
> Message-ID:
> <926abad51002261231g71b81d30o48b7ab63f41ba820 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Phenix developers/gurus,
> I got a SAD structure, the experimental map (overall_best_denmod..mtz) from
> Autosol looks great. I then built the model and used phenix.refine to
> refine
> the model using the "exptl_fobs....mtz", which worked well as shown by the
> lowered Rfree. However, the map from the refinement makes no sense at all,
> totally featureless. Using the same refined model and mtz,
> phenix.model_vs_data did make the right map. I have tried both phenix 1.5
> and 1.6. Any clue?
> Thanks,
> Xuewu Zhang
> UT Southwestern Medical Center
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> ------------------------------
>
> Message: 4
> Date: Fri, 26 Feb 2010 12:39:26 -0800
> From: Paul Adams <PDAdams at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Map after refinement
> Message-ID: <2A8140BF-342E-42B4-B242-A87C07A2C0E0 at lbl.gov>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> Are you using a CNS format map in coot by any chance?
>
> On Feb 26, 2010, at 12:31 PM, Xuewu Zhang wrote:
>
> > Hi Phenix developers/gurus,
> > I got a SAD structure, the experimental map
> > (overall_best_denmod..mtz) from Autosol looks great. I then built
> > the model and used phenix.refine to refine the model using the
> > "exptl_fobs....mtz", which worked well as shown by the lowered
> > Rfree. However, the map from the refinement makes no sense at all,
> > totally featureless. Using the same refined model and mtz,
> > phenix.model_vs_data did make the right map. I have tried both
> > phenix 1.5 and 1.6. Any clue?
> > Thanks,
> > Xuewu Zhang
> > UT Southwestern Medical Center
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
> --
> Paul Adams
> Acting Division Director, Physical Biosciences Division, Lawrence
> Berkeley Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Head, Berkeley Center for Structural Biology
>
> Building 64, Room 248
> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Patty Jimenez [ PAJimenez at lbl.gov ]
> [ 1-510-486-7963 ]
> --
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 26 Feb 2010 13:43:39 -0800
> From: Pavel Afonine <PAfonine at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Map after refinement
> Message-ID: <4B88408B.3030900 at lbl.gov>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi,
>
> I heard about this scenario of getting a nonsensical map a couple of
> times before, however I was never able to reproduce this problem myself.
>
> Could you please send me (to my email address, not to the whole bb) the
> phenix.refine inputs so I can reproduce this problem and fix it?
> Specifically, I need: model and data files, and the exact command that
> leads to bad maps. All files will be handled confidentially.
>
> I guess the problem is in HL coefficients that are used by phenix.refine
> to output phase-combined map. model_vs_data does not use HL coefficients
> and this possibly explains the difference. If it is the case then we
> would need to figure out what happens to HL coefficients and this would
> require us to reproduce your Autosol run.
>
> Thanks!
> Pavel.
>
>
> On 2/26/10 12:31 PM, Xuewu Zhang wrote:
> > Hi Phenix developers/gurus,
> > I got a SAD structure, the experimental map (overall_best_denmod..mtz)
> > from Autosol looks great. I then built the model and used
> > phenix.refine to refine the model using the "exptl_fobs....mtz", which
> > worked well as shown by the lowered Rfree. However, the map from the
> > refinement makes no sense at all, totally featureless. Using the same
> > refined model and mtz, phenix.model_vs_data did make the right map. I
> > have tried both phenix 1.5 and 1.6. Any clue?
> > Thanks,
> > Xuewu Zhang
> > UT Southwestern Medical Center
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> >
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> ------------------------------
>
> Message: 6
> Date: Fri, 26 Feb 2010 17:29:08 -0500
> From: David Garboczi <dgarboczi at niaid.nih.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: [phenixbb] weaker density in maps
> Message-ID: <p06240800c7adedc01541@[137.187.157.12]>
> Content-Type: text/plain; charset="us-ascii" ; format="flowed"
>
> We sometimes build model into density at ~0.8 sigma, refine, and the
> Rfree becomes lower. So we believe that we put model where it should
> be.
>
> Running the same data and same model in phenix under default
> conditions at the command line, we obtain maps that do not show the
> weaker features in which we believe in CNS.
>
> We are wondering if we can believe the weaker density or is it that
> we are not toggling something on in phenix.
>
> We routinely view the phenix-generated maps after transforming them
> to dsn6 files in mapman.
>
> thanks,
> Dave
>
>
> --
>
>
> ------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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>
> End of phenixbb Digest, Vol 51, Issue 31
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