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, 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)

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Message: 1 Date: Fri, 26 Feb 2010 18:17:06 -0200 From: Alejandro Buschiazzo To: PHENIX user mailing list Subject: [phenixbb] Int'l Workshop on Macromolecular Crystallography - South America Message-ID: <[email protected]> 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 : [email protected]

*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 [email protected]

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

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Message: 2 Date: Fri, 26 Feb 2010 22:18:33 +0200 From: Felix Frolow To: PHENIX user mailing list Subject: Re: [phenixbb] Gap between R and Rfree Message-ID: 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: [email protected] 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

...

...

*** 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

Rfree-Rwork. For example: 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

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 >> [email protected] >> http://phenix-online.org/mailman/listinfo/phenixbb >> > _______________________________________________ > phenixbb mailing list > [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] 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 To: [email protected] Subject: Re: [phenixbb] Map after refinement Message-ID: <[email protected]> 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