- phenixbb - phenix-online.org

phenix.reduce segmentation fault with -trim option on Snow leopard Mac OSX
by hari jayaram 04 Mar '10

04 Mar '10

Hi I am running the phenix.reduce with the -trim option and getting a segmentation fault with phenix version 1.6.289 I will remove the molprobity introduced hydrogens using pdbtools ..but thought I will write in with this Thanks Hari $ phenix.reduce s3-3_2.1_refmac0-coot-15_refmac0FH.pdb -trim > s3-3_2.1_refmac0-coot-15_refmac0FnoH.pdb reduce: version 3.15 11/6/2009, Copyright 1997-2009, J. Michael Word Processing file: "s3-3_2.1_refmac0-coot-15_refmac0FH.pdb" Segmentation fault

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coot integration require coot with python?
by hari jayaram 03 Mar '10

03 Mar '10

Hi Is it likely that the phenix-coot integration with the new GUI requires a python infused coot ?. Although I have set the coot path correctly nothing happens after coot launches . I am using the ccp4 6.1.3 coot 0.6 (revision 2540) [with guile 1.8.3 embedded] and phenix 1.6.289 on OSX snow leopard 10.6.2. I know the ccp4 coot does not come with python scripting support ...the pymol integration seems fine , but coot just sits there with an empty window after a phenix.validate run. Any ideas on how to have them talking to each other? Thanks Hari

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autosol and NCS
by hli＠uci.edu 03 Mar '10

03 Mar '10

I have solved a structure by MR with Phaser. There are 4 copies of molecules per ASU. Parts of the search model are not agreeable with the new structure leading to messy density in some regions. Now a set of SAD data has been collected. I want to run Autosol (MRSAD) to combine the SAD and model phases, doing density modification including the NCS. Can I run simple_ncs_from_pdb to get the NCS operators from the MR solution pdb file and use them for Autosol? Thanks for help. Huiying UC Irvine

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Phaser phasing power statistics
by Daqi Tu 03 Mar '10

03 Mar '10

Hi, I was trying to find phasing power statistics from phenix.autosol log file but couldn't. My structure was phased by Phaser SAD module in phenix.autosol, all I could find was figure of merit. I then ran Phaser SAD within CCP4 and still could not find phasing power statistics from its log. Does anyone know if Phaser SAD generates phasing power statistics in its log file at all? Thanks. Daqi Tu Postdoc Eck lab Harvard medical school

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SAD + Xray = ???
by J. Fleming 02 Mar '10

02 Mar '10

Hi, I have a set of Se-Met SAD data, high resolution x-ray data, and a protein sequence. Is there a way to combine these data sets in Phenix and carry out an autobuild? I saw a section in the manual about MRSAD but that requires a starting model. I've used the SAD data alone to generate a model but I'd like to use both data sets together. Thanks for your thoughts, -Jon

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ICCBM13 - Call for abstracts now open!
by Valerie Pye 02 Mar '10

02 Mar '10

Apologies for this being off topic - but may be of general interest: * * * * *13th International Conference on the Crystallisation of Biological Macromolecules* Trinity College Dublin, Ireland 12th – 16th September 2010 *Crystallization Workshop* – 9th – 12th September 2010 Call for Abstracts Now Open <http://www.iccbm13.ie/abstracts.html> The *13th International Conference on the Crystallisation of Biological Macromolecules* (*ICCBM13 <http://www.iccbm13.ie/>*) is the meeting of choice to learn about the latest research and developments in biomacromolecular crystallogenesis for structure-function-rational design applications. At ICCBM13 leading academic and pharmaceutical scientists will report on challenging systems to include macromolecular complexes and membrane proteins with an emphasis on novel practical as well as mechanistic aspects of crystallogenesis. To cater to the needs of the individual wanting to learn how to grow crystals or to acquire new crystallisation skills, the Conference is preceded by a *Workshop <http://www.iccbm13.ie/workshop.html>* devoted to hands-on instruction on select aspects of macromolecule production and crystal growth. The Conference will be held at *Trinity College Dublin <http://www.tcd.ie/>, Ireland* from the 12th to the 16th September 2010. Convenient and affordable housing is available on and around Trinity College. The campus is situated in the heart of Ireland’s capital city and is surrounded by a diversity of restaurants, pubs, theatres and other points of interests. *Scholarships <http://www.iccbm13.ie/scholarships.html>* are available to Graduate Students and Postdoctoral Fellows. Additional information is available at *www.iccbm13.ie* *ICCBM13 Congress Secretariat* T: + 353 (0) 1 400 3626 F: + 353 (0) 1 400 3692 E: info(a)iccbm13.ie W: www.iccbm13.ie *C/O Keynote PCO* Suite 26, Anglesea House, Blackrock Co. Dublin, Ireland www.keynotepco.ie

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twin refinement
by subhash bihani 02 Mar '10

02 Mar '10

Hi i am refining a protein strucutre with space group P61. Intesity statistics doesnot suggest any twining but refmac and phenix xtriage suggest a twin operator with fraction 0.48. when refined with this twin operator R factors come dowm by 3-5% and also map looks much better. but upon closer inspceion it seems that maps are heavily biased toward the model in both refmac and phenix ( I have mutated one lysine to his and it changed the map to cover his). my question is why twin refinement maps are biased and what are the ways to overcome this. my second question is how to decide whether to use twin refinement or not. is it depends on R factor statistics or we have to check some other parameters. thanks in advance subhash bihani scientific officer Bhabha Atomic Research Centre Trombay-400085 Mumbai(M.S.) India Ph. +912594688 (o) +919322191020 -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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NCS restraints
by Mirek Cygler 28 Feb '10

28 Feb '10

Hi, I have NCS symmetry in my crystal and wouldlike to use it during the refinement. What is the strength of the restraints for the backbone, for the sidechains? How can I control these restraints? Thanks, Mirek

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Clarification on ADPs in PDB files for TLS refinement ?
by Phil Jeffrey 27 Feb '10

27 Feb '10

Hi, Having a discussion with a colleague yesterday on differences in Phenix and Refmac representations of TLS B-factors in the PDB file I came across two different definitions for what the PDB ANISOU U's correspond to as written by Phenix: 1. From necat.chem.cornell.edu/workshops/.../WK04_PavelAfonine.pdf on p.20 U(TOTAL)= U(ATOM) + U(TLS) + U(CRYST) and only U(atom) + U(tls) is stored in the PDB ANISOU card. 2. From http://proteincrystallography.org/ccp4bb/message8948.html "Utotal = Utls + Ulocal + Ucryst. So, the ANISOU records always contain Utotal and ATOM records contain isotropic equivalent of Utotal" Which is not the same thing. I suspect it's #1. Am I right ? I would think that U(cryst) is potentially a non-zero contribution to atomic ANISOU values but is actually applied before the TLS/Anisotropic B-factors are refined. As a tie-breaker between #1 and #2 the program documentation suggest that it is just U(tls)+U(atom) but the paragraph that nominally explains it is not short of of inconsistencies, referring to the ANISOU record as having the "the total B-factor (B_tls + B_individual)" whereas they're not only not B's (they are U's) but it's also not the *total* U or B by its own definitions. IMHO it would warrant a rewrite for clarity since B and U are used interchangeably and "total" has variable usage. Phil Jeffrey Princeton

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Re: [phenixbb] Map after refinement
by Xuewu Zhang 26 Feb '10

26 Feb '10

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(a)phenix-online.org> wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > 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(a)pasteur.edu.uy> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Int'l Workshop on Macromolecular Crystallography - > South America > Message-ID: <4B882C42.9080701(a)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(a)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(a)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(a)post.tau.ac.il> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Gap between R and Rfree > Message-ID: <F52C4FE8-AE34-4C23-B74E-A923995E5831(a)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(a)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(a)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(a)phenix-online.org > >>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>>>>> > >>>>>> _______________________________________________ > >>>>>> phenixbb mailing list > >>>>>> phenixbb(a)phenix-online.org > >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>>> _______________________________________________ > >>>>> phenixbb mailing list > >>>>> phenixbb(a)phenix-online.org > >>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>> _______________________________________________ > >>>> phenixbb mailing list > >>>> phenixbb(a)phenix-online.org > >>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> > >>> _______________________________________________ > >>> phenixbb mailing list > >>> phenixbb(a)phenix-online.org > >>> http://phenix-online.org/mailman/listinfo/phenixbb > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > ------------------------------ > > Message: 3 > Date: Fri, 26 Feb 2010 14:31:26 -0600 > From: Xuewu Zhang <xuewu.zhang(a)gmail.com> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Map after refinement > Message-ID: > <926abad51002261231g71b81d30o48b7ab63f41ba820(a)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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