UT Southwestern Medical Center

On Fri, Feb 26, 2010 at 4:29 PM, <phenixbb-request@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@pasteur.edu.uy>
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: [phenixbb] Int'l Workshop on Macromolecular Crystallography -
South America
Message-ID: <4B882C42.9080701@pasteur.edu.uy>
Content-Type: text/plain; charset=windows-1252; format=flowed

Dear colleagues,

just a reminder, we're close to the deadline for applications. Details
below.

Thank you!

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

*International Workshop ?Macromolecular Crystallography : Introduction
and Applications"*

*April 26 - May 7, 2010*

*Institut Pasteur de Montevideo*

*Uruguay*

The principal aim of this course, is to give intense hands-on training
in all main aspects of macromolecular 3D structure determination by X
ray diffraction.

The course will include lectures delivered by a number of
international experts in the discipline, linked to hands-on
experimental work and demonstrations.

Special emphasis will be given to :

* Experiment design : manual and robotic crystallogenesis of
macromolecules, X ray diffraction of single crystals, data collection
* Diffraction data processing
* Model refinement and structural analysis

*ACTIVITY INTENDED FOR*

* Graduate Students (MSc and PhD)
* Postdocs
* Young Research Scientists

*APPLICATION REQUIREMENTS*

Candidates should send the following information :

1. -Short CV (including age, current position, scientific interests,
publications)
2. -Letter of motivation (the applicant should stress how
Macromolecular Crystallography is included in her/his ongoing
scientific project)
3. -Reference letter from the apllicant's supervisor

*SCHOLARSHIPS*

Inscription fees are fully covered for all accepted students.
Applicants from abroad with no financial support, are welcome to apply
for a lodging and per diem expenses scholarship. This should be
inlcuded as a separate document at the time of application. A limited
number of traveling aids will be available: arguments backing this
request should be duly explained, to be evaluated on a case by case
basis.

*APPLICATION DEADLINE*

All applications should be received until March 7 2010. They should be
sent as a single pdf document to : crystallography@pasteur.edu.uy

*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
Institut Pasteur de Paris

Dr. William Shepard
Proxima 2
Synchrotron Soleil

For further information, please E-mail to crystallography@pasteur.edu.uy

The official language of the course will be english.

Detailed information is available at:
http://www.pasteur.edu.uy/mxcourse Please check for regular updates of
the program.

*FUNDING*

RIIP, AMSUD/PASTEUR, IP MONTEVIDEO (URUGUAY INNOVA), CeBEM

This International Workshop is part of the activities of the Center of
Structural Biology of Mercosur (Centro de Biolog?a Estructural del
Mercosur - CeBEM)

--
Alejandro Buschiazzo, PhD
Research Scientist
Laboratory of Protein Crystallography
Pasteur Institute of Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY

Phone: +5982 5220910 int. 120
Fax: +5982 5224185

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

Message: 2
Date: Fri, 26 Feb 2010 22:18:33 +0200
From: Felix Frolow <mbfrolow@post.tau.ac.il>
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] Gap between R and Rfree
Message-ID: <F52C4FE8-AE34-4C23-B74E-A923995E5831@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@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@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@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@gmail.com>
To: phenixbb@phenix-online.org
Subject: Re: [phenixbb] Map after refinement
Message-ID:
<926abad51002261231g71b81d30o48b7ab63f41ba820@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@lbl.gov>
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] Map after refinement
Message-ID: <2A8140BF-342E-42B4-B242-A87C07A2C0E0@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@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@lbl.gov ]
[ 1-510-486-7963 ]
--

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

Message: 5
Date: Fri, 26 Feb 2010 13:43:39 -0800
From: Pavel Afonine <PAfonine@lbl.gov>
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] Map after refinement
Message-ID: <4B88408B.3030900@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@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@niaid.nih.gov>
To: PHENIX user mailing list <phenixbb@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

--

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