- phenixbb - phenix-online.org

Meeting Announcement: Northwest Crystallography Workshop
by Dale Tronrud 07 Feb '14

07 Feb '14

(Pacific) Northwest Crystallography Workshop http://oregonstate.edu/conferences/event/nwcw2014/ June 20-22, 2014 Registration is now open for this year's edition of the Northwest Crystallography Workshop. It is being hosted at Oregon State University in Corvallis in the heart of the Willamette Valley surrounded by wine country, wildlife refuges, and with both the Cascade Mountains and the Pacific Ocean within easy driving distance. It can be easily accessed from either the Portland or Eugene airports. This biennial meeting has been held at various locations in the Pacific Northwest since 1981. It has always proven to be a great venue to meet other researchers in the region who are interested both in using macromolecular crystallography to solve structures and in developing and enhancing methods. The "workshop" part of the name will be taken seriously. We will have talks and posters with priority for speaking slots given to students and post-docs who focus on methodologies or interesting structure determination stories, and/or how structural observations provide insight into function and biology. There will be a reception on Friday evening. On Saturday there will be talks during the day and a banquet followed by a keynote address in the evening. Talks will continue on Sunday morning with the workshop wrapping-up at noon. A light lunch will be served on Saturday and a boxed lunch will be available on Sunday. Register today and get your abstracts submitted anytime between now and the April 30 abstract deadline. We've tried to keep registration costs low and early registration (through April 30) is $75 for students and $100 for others. Reasonably priced on-campus dormitory housing is available and must be arranged at the time of registration. Special rates at two local hotels have been arranged for those who want to book their own lodgings. We look forward to a great meeting and celebration of the International Year of Crystallography. Dale and Andy Dale E. Tronrud and P. Andrew Karplus Department of Biochemistry & Biophysics 2011 ALS Bldg Oregon State University Corvallis, OR 97331 USA

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how to remove hydrogen from pdb
by Afshan Begum 07 Feb '14

07 Feb '14

Dear Experts, Could you kindly tell me how can i remove hydrogen from my coordinate. Actually i refine my structure with phenix along all hydrogen now its almost done but before submitting the molecule into PDB data bank i want to remove hydrogen from the coordinate which i do not know how to do, suggestion would be appreciated Best Regards AFSHAN =========================================== Dr. Afshan Begum

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weight_selection_criteria
by Mark A Saper 06 Feb '14

06 Feb '14

Can anyone explain what the weight_selection_criteria parameters (see below)? How do they interact with other weights. Are they still used if I set optimize_xyz_weight=TRUE? I'm using dev-1616. target_weights optimize_xyz_weight= False optimize_adp_weight= False wxc_scale= 0.5 wxu_scale= 1.0 wc= 1.0 wu= 1.0 fix_wxc= None fix_wxu= None shake_sites= True shake_adp= 10.0 regularize_ncycles= 50 verbose= 1 wnc_scale= 0.5 wnu_scale= 1.0 rmsd_cutoff_for_gradient_filtering= 3.0 force_optimize_weights= False weight_selection_criteria bonds_rmsd= None angles_rmsd= None r_free_minus_r_work= None r_free_range_width= None mean_diff_b_iso_bonded_fraction= None min_diff_b_iso_bonded= None Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan c/o Biophysics, Chem 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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phenix version 1.8.4
by Rosario Recacha 06 Feb '14

06 Feb '14

Hello, I installed the last version if phenix in ubuntu and whe I want to run it I receive the next message: ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory I installed older versions in other computers following the same indications, and never I have had problems. Thanks in advance. Kind Regards, Rosario

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phenix.autosol and phenix.hyss now optimized for weak SAD data
by Terwilliger, Thomas C 06 Feb '14

06 Feb '14

Hi Phenix users! You might notice some big differences in HySS and AutoSol in the new 2014 versions of Phenix (starting with current nightly builds and the soon-to-be-released Phenix-1.8.5). The big changes are parallelization, the use of Phaser completion in HySS, iterative Phaser completion using maps and models in AutoSol, and on-the-fly optimization of parameters in AutoSol for cases with weak anomalous signal. Now HySS and AutoSol can solve structures with very weak SAD phase information that previous versions could not solve. More details will be in the Phenix newsletter that will come out shortly! You can see documentation on the new HySS at: http://phenix-online.org/version_docs/dev-1613/hyss.htm#anch8 and on the new AutoSol at: http://phenix-online.org/version_docs/dev-1613/autosol.htm#anch118 --Tom Terwilliger, Randy Read, Gábor Bunkóczi, Nat Echols

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Computational Crystallography Newsletter - Volume 5, Number 1
by Nigel Moriarty 05 Feb '14

05 Feb '14

Dear Colleagues, I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. Articles -------- FEL Detectors and ImageCIF Quantum Mechanics-based Refinement in Phenix/DivCon Short communications -------------------- Short Communications Phenix tools for interpretation of BIOMT and MTRIX records of PDB files Coping with BIG DATA image formats: integration of CBF, NeXus and HDF5 Fitting tips #7 - Getting the Pucker Right in RNA Structures Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Fwd: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 04 Feb '14

04 Feb '14

---------- Forwarded message ---------- From: Nukri Sanishvili <rsanishvili(a)anl.gov> To: <phenixbb(a)phenix-online.org> Date: Mon, 3 Feb 2014 18:12:09 -0600 Subject: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php<https://mail.anl.gov/owa/redir.aspx?C=Qww5V7BVpECZd8A2kldFSf7_-DvC9NAIxdFZE…> *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<https://mail.anl.gov/owa/redir.aspx?C=Qww5V7BVpECZd8A2kldFSf7_-DvC9NAIxdFZE…> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri -- Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667rsanishvili(a)anl.gov

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Re: [phenixbb] autosol error// phaser error
by Terwilliger, Thomas C 03 Feb '14

03 Feb '14

Hi Almudena, Can you possibly say what version of Phenix you are using: phenix.version and then the columns in your mtz file: phenix.mtz.dump my_mtz_that_fails.mtz and the inputs you used for autosol and phaser (you can send the top part of the log files that should have this information). Can you also try this little test for resolve model building (that is where the "cannot read segment library" comes from): phenix_regression.wizards.test_command_line_build test_autobuild_quick That would help for diagnosing the problems. All the best, Tom T Hi everyone, I am facing some troubles with PHASER and with AutoSol (things that did not happen earlier to me). I am working with anomalous data and the first thing I do is to run HySS in order to find the heavy atoms sites. Once this is done I have two options: run PHASER or run AutoSol. Phaser gives the following error message: ERROR setting up data inputs (FATAL RUNTIME) Can not find MTZ column "F_SAD_SAD(+)" Instead Autosol gives the following: ERROR sorry can not read segment library Could anyone help me out here? Thank you very much in advance. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Ten days left, many seats available: Apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 31 Jan '14

31 Jan '14

We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2014: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Output bulk solvent
by Koji Yonekura 29 Jan '14

29 Jan '14

Dear All, I am wondering if Phenix.refine has an option to output bulk solvent F to the mtz file. Best regards, Koji -- Koji Yonekura, Ph. D. Biostructural Mechanism Laboratory RIKEN SPring-8 Center Harima Institute 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan Tel: +81-791-58-2837 Fax: +81-791-58-1844 PHS: +81-791-58-0803 (7803) E-mail: yone(a)spring8.or.jp http://www.riken.jp/biostrmech/

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Postdoctoral position in macromolecular crystallography, HZI Braunschweig, Germany
by Wulf Blankenfeldt 27 Jan '14

27 Jan '14

Postdoctoral Position in Macromolecular Crystallography The Helmholtz Centre for Infection Research (HZI) in Braunschweig (Germany) announces an opening for a postdoctoral researcher in macromolecular crystallography. The position is associated with the department “Structure and Function of Proteins” headed by Prof. Wulf Blankenfeldt. The department focuses on unraveling molecular mechanisms of uncharacterized processes in the metabolism, regulation and virulence of pathogenic microorganisms. About the institute More than 800 people work at the HZI, a research institution in the Helmholtz Association of German Research Centres funded jointly by the Federal Republic of Germany and the Federal State of Lower Saxony. The centre’s task is to undertake biomedical research in the field of infection biology to expand knowledge of the fundamental mechanisms behind medically relevant infectious diseases with the aim of providing the key for the development of new therapeutics and vaccines. The Department “Structure and Function of Proteins” offers excellent working conditions, state-of-the-art technical platforms and equipment (including bacterial, insect cell and mammalian protein expression systems; access to a rotating anode X-ray source and several synchrotrons, crystal imaging and liquid handling systems; biophysical characterization of proteins), a lively scientific community and excellent support for the development of personal soft-skills. Projects All projects in our department aim at the identification and elucidation of the molecular function and mechanism of uncharacterized genes in pathogenic microorganisms. A better understanding of these “white spaces” of the genome map will not only unravel interesting new molecular processes but also provide novel targets for pharmaceutical intervention. To achieve our goal, we employ a gamut of methods including – in addition to structural biology – microbiological, biophysical and metabolomic techniques. Because our department is also the prime partner for structural biology-related questions at the HZI, the Technical University of Braunschweig and the German Centre for Infection Research (http://www.dzif.de/en/) the successful candidate will have the opportunity (and is expected) to take leading roles within our existing and emerging collaborations. Prerequisites Candidates should hold a Ph.D. in a life sciences related subject at the time of their employment. They should have a strong background in all aspects of macromolecular crystallography, including techniques of recombinant protein production and biophysical characterization. Experience in handling and manipulating pathogenic bacteria (biosafety level 2) is a plus. The handicapped Qualified applicants with a disability will be given preference. Job details The position is available immediately for three years with a six month probation period. Salary is according to level E14 of the collective labor agreement for public service (TVöD). Application details Candidates are asked to submit a full CV including a publication list, a cover letter outlining their interest in this position, a brief summary of current and past research experience (max. 2 pages) and contact data of at least two referees. All documents and information should be provided in English or German. Applications should refer to code 05/2014 and be sent by 28.02.2014 to: Helmholtz Centre for Infection Research Dept. of Human Resources Inhoffenstraße 7 38124 Braunschweig Germany E-Mail: JobsHZI(a)helmholtz-hzi.de For further information, please contact Prof. Dr. Wulf Blankenfeldt, phone: +49-531-6181-7000, e-mail: wulf.blankenfeldt(a)helmholtz-hzi.de ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Re: [phenixbb] measuring the angle between two DNA duplexes
by Xiang-Jun Lu 26 Jan '14

26 Jan '14

Hi Xiang, Since you mentioned "or in other software", I think I can chime in to this topic. The short answer is to see "How to calculate DNA bending angle?" ( http://forum.x3dna.org/faqs/how-to-calculate-dna-bending-angle/). 3DNA, following the original NewHelix algorithm, calculates a best-fitted linear global helix (where sensible) using equivalent C1'...C1', RN9/YN1...RN9/YN1 atom pairs along each strand. The so-called global helical axis parameters are no longer widely used, but the best-fitted linear helical axis is a useful concept, and has been kept in 3DNA and DSSR [ http://forum.x3dna.org/rna-structures/dssr-software-for-defining-the-(secon… ]. HTH, Xiang-Jun -- Xiang-Jun Lu (PhD) Email: xiangjun(a)x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ > > > On 1/20/14, 5:48 AM, ?? wrote: > > > > Hi, > > > > I have a DNA model which is composed of two DNA duplexes. I want to > > measure the angle between the two duplexes and if there a way to do it in > > PHENIX or in other software? > > > > Thanks you very much for your help! > > > > Sincerely, > > Xiang > > > > -- > > Li Xiang > > Department of chemistry, > > Purdue University > > Email?lixiang1642(a)gmail.com > >

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non-bonded
by Leonard Thomas 23 Jan '14

23 Jan '14

Hello All, We are trying to refine a complex that was solved using Phaser. We have run a round of rigid body refinement using Refmac and now want to run a simulated annealing run in Phenix. Visually the complex looks pretty. The resolution we currently are at is 3.6 A. When we go to run phenix.refine the program quits with a Number of non-bonded interactions < 0.0001 error. Is there a way to loosen this up a bit or get around it or should we go about this in a different way? Best Regard, Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu http://barlywine.chem.ou.edu http://structuralbiology.ou.edu

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measuring the angle between two DNA duplexes
by 李翔 22 Jan '14

22 Jan '14

Hi, I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software? Thanks you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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phenix.refine wxc weight
by rainfieldcn 17 Jan '14

17 Jan '14

Hi All, I am doing refinement on some low resolution structures ( around 4A ). I used wxc_scale=0.15 before on phenix.refine: 1.8.2_1309 I got: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 BOND : 0.006 0.048 24993 REMARK 3 ANGLE : 1.049 11.841 33849 REMARK 3 CHIRALITY : 0.044 0.323 3843 REMARK 3 PLANARITY : 0.005 0.053 4276 REMARK 3 DIHEDRAL : 14.080 87.581 8889 REMARK 3 MIN NONBONDED DISTANCE : 2.098 REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 10.49 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.10 % REMARK 3 ALLOWED : 3.84 % REMARK 3 FAVORED : 96.06 % REMARK 3 ROTAMER OUTLIERS : 3.87 % REMARK 3 CBETA DEVIATIONS : 0 now, phenix is updated to phenix.refine: 1.8.4_1496. and I got: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 BOND : 0.016 0.237 24993 REMARK 3 ANGLE : 2.262 36.773 33853 REMARK 3 CHIRALITY : 0.099 2.724 3847 REMARK 3 PLANARITY : 0.010 0.102 4280 REMARK 3 DIHEDRAL : 14.585 89.962 8889 REMARK 3 MIN NONBONDED DISTANCE : 1.923 REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 17.57 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.32 % REMARK 3 ALLOWED : 4.07 % REMARK 3 FAVORED : 95.61 % REMARK 3 ROTAMER OUTLIERS : 4.22 % REMARK 3 CBETA DEVIATIONS : 39 So I am wondering if there is some bug in phenix.refine that wxc_scale doesn't work? Thanks, Lei

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MR
by Swastik Phulera 17 Jan '14

17 Jan '14

Dear All, I am trying an MR, it looks like there would be 16 dimers in the asymmetric unit, Upon running Phaser once it could easily fit two copies. I now wish to use this solution to perform further MR runs in order to locate the other dimers. I was just wondering what shall be the right way to go about it. Regards Swastik

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Re: [phenixbb] phenixbb Digest, Vol 98, Issue 2
by Kay Diederichs 14 Jan '14

14 Jan '14

Am 14.01.14 21:00, schrieb phenixbb-request(a)phenix-online.org: > PS. It's possible I'm still misunderstanding the meaning of FRIEDEL'S_LAW=TRUE. > Under what circumstances does XDS output anomalous vs. non-anomalous data? This keyword affects the way the statistics are calculated in CORRECT.LP: with FRIEDEL'S_LAW=FALSE the members of Bijvoet pairs are treated as separate reflections, which almost doubles the number of unique reflections, affecting the reported completeness and R-values, I/sigmas and so on. The reflection output file XDS_ASCII.HKL has unmerged intensities in all cases (whether FRIEDEL'S_LAW=TRUE or FALSE). Phenix should ignore the FRIEDEL'S_LAW setting in XDS_ASCII.HKL. hope this helps, Kay

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XDS data
by Tim Gruene 14 Jan '14

14 Jan '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I would like to run Phaser-EP through the phenix GUI. When I first uploaded the XDS_ASCII.HKL file, there was an error message about "No valid observed reflections found in this file". Subsequently I uploaded an unmerged hklf4 file. The GUI tells me I need to let phenix know about it being hklf4 by appending '=hklf4'. However, when I do so, there is an error message the file did not exist and the Data file line goes red. Where should I correctly append '=hklf4'? At the bottom, the message states it would be best to recover the original reflection data such as [...] XDS [...]. This suggests that the original XDS_ASCII.HKL could be used. Is this correct in if so, how do I put it into phenix? Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFS1TDEUxlJ7aRr7hoRArKdAKDpXBrs4wsWMvWw0JNo8F746fY76ACfeFuG geGY6T6se8peE9dEGz8ETow= =AaLk -----END PGP SIGNATURE-----

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Refining coordinates
by Subhani Bandara 10 Jan '14

10 Jan '14

Dear all, I have a protein crystallized with metal chelate complexes and some of the atoms of chelators and the metals sit on the two fold axis. Is there a way that I can refine the coordinates of those atoms only along the two fold axis (let's say X) while restraining the coordinate refinement along other two axes (Y and Z)? Thanks Subhani

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fwd: Announcement: International Summer School of Crystallography - May 2014, Hamburg, Germany
by Nathaniel Echols 10 Jan '14

10 Jan '14

---------- Forwarded message ---------- From: "Oberthuer, Dominik" <dominik.oberthuer(a)cfel.de> To: phenixbb(a)phenix-online.org Date: Fri, 10 Jan 2014 16:14:08 +0100 Subject: Announcement: International Summer School of Crystallography - May 2014, Hamburg, Germany Dear colleagues, we are pleased to announce the first International Summer School of Crystallography at the Center for Free-Electron Laser Science at DESY, Hamburg (D). As part of the International Year of Crystallography 2014, Prof. Carmelo Giacovazzo will give a full week of lectures on the basics of crystallography, as well as the basics of modern phasing methods in protein crystallography. The course will cover basic mathematical understanding of crystallographic point and space groups, diffraction experiments, structure factor calculations, systematic absences, determination of space groups and many additional topics. After the discussions of theory, one afternoon will be spent to learn about modern applications of protein crystallography using advanced light sources, such as 3rd generation synchrotron and XFELs. The course will be given mainly for PhD students working in the field of crystallography, but exceptions for motivated PostDocs and MSc students can be made. The course will mostly cover mathematical background of crystallography, hence we are looking for students, having a (bio)physics background. This will NOT be a workshop covering protein crystallographic programs but rather the theory behind those programs. The course will start Sunday (11.05.2014) around lunch and will end Saturday (17.05.2014) around lunch. The registration fee is 100 EUR per person including coffee breaks and lunch. Accommodations can be made at the DESY Guest House: 70 EUR per person for 7 nights (10.-17.05.2014). Application deadline will be 28th of February 2014 and notification of accepted applications will be sent during March 2014. The applications will be managed via the DESY Indico system: https://indico.desy.de//event/ISSC14 Applicants must provide a motivation letter, as well as a CV, directly to the organizer Cornelius Gati (cornelius.gati(a)cfel.de). Places and accommodation are limited to 30 students in total. Please contact Cornelius Gati regarding further questions ( cornelius.gati(a)cfel.de). We are looking forward to welcome you in Hamburg! -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science Coherent Imaging Division and University of Hamburg Laboratory for Structural Biology of Infection and Inflammation Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de obertuer(a)chemie.uni-hamburg.de

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Low F-obs Values
by 张怀东 07 Jan '14

07 Jan '14

Hi, everyone I used phenix-1.8.2-1309 to do MR and Autobuild, then Refinement, the max F-obs value of the mtz file from refinement was about 300. However, I used phenix-1.8.4-1496 to do the same work, the max F-obs value was about 3000. The resulting structure models donot seem to be any different. We tried several datasets of different proteins, and the max F-obs value are low with phenix-1.8.2-1309. So is this a real problem or not? Best regards Huaidong Zhang

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I remind you: Please apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 06 Jan '14

06 Jan '14

We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2014: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Postdoc positions (SGC, Diamond): fragments into crystals
by Frank von Delft 02 Jan '14

02 Jan '14

Hello, I have 3 open postdoc positions, to work on technologies around fragment screening in crystals, which is what my (joint) research team at Diamond (beamline I04-1) and SGC (PX group) is trying to make simple and accessible. Details of the project are on my website <http://www.thesgc.org/scientists/groups/oxford/crystallography>; we need smart people to: * (at SGC) test-drive with start-to-end soaking campaigns <http://www.thesgc.org/careers/oxford/crystallography-postdoc-fragment-scree…> * (at SGC) develop crystal engineering to get soakable systems (molecular biology, biochemistry) <http://www.thesgc.org/careers/oxford/crystallography-postdoc-crystal-engine…> * (at Diamond) explore soaking techniques <http://www.diamond.ac.uk/Home/Jobs/Current/DIA0886_CH.html> The application deadlines for the SGC posts are a function of the UK's charming political climate; if you're interested but from outside the EU, alert me with a direct email plus CV. phx. P.S. if you know smart undergrads who'd be interested in a DPhil in that sort of thing -- applied engineering, technology -- send them to that website too. (DPhils are what you get in Oxford - that makes it special. Or "special".)

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Multiple conformation, two ligands
by YANG HAI 01 Jan '14

01 Jan '14

Dear Phenix Community, I tried to model two ligands one of which has two conformations. In other words, the two scenarios are: 1) ligand X with conformation A (XA, 75% occupancy); 2) ligand X with conformation B (XB, 25% occupancy) plus another ligand Y. However, the problem is ligand Y will have steric clash with ligand XA. If I rename ligand X and Y to the same residue name then I do not know how to define the CIF file. I apologize if this question was asked before and I do not know how Phenix or other refinement can deal with multiple conformation a group of ligands. Thanks. Happy new year! Yang Hai Christianson Lab University of Pennsylvania

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phenix morph- no shift problems
by Ming Sun 29 Dec '13

29 Dec '13

Hi Everyone I'm currently trying running phenix.morph model on a large complex. However, after 5 cycles of running, there were no shift at all. And we set data, model, map_coeffs, reference_restraints, morph_main.. Does anyone happen to have similar issues? Any specific parameter I should change? Thanks again -Ming

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Reduce NQH
by jp d 20 Dec '13

20 Dec '13

hi, we were going through the logs recently and see something odd during Reduce N/Q/H analysis the log file looks like this: ================================== NQH flips ================================== r_work=0.3047 r_free=0.3518 Analyzing N/Q/H residues for possible flip corrections... segID AL01 renamed chain A for Reduce N/Q/H analysis segID AL02 renamed chain B for Reduce N/Q/H analysis ... segID AL29 renamed chain Y for Reduce N/Q/H analysis segID AL30 renamed chain Z for Reduce N/Q/H analysis segID AL32 renamed chain a for Reduce N/Q/H analysis segID AL33 renamed chain a for Reduce N/Q/H analysis segID AL34 renamed chain b for Reduce N/Q/H analysis segID AL35 renamed chain b for Reduce N/Q/H analysis ... segID BL28 renamed chain z for Reduce N/Q/H analysis segID BL31 renamed chain z for Reduce N/Q/H analysis segID BL13 renamed chain AA for Reduce N/Q/H analysis segID BL29 renamed chain AB for Reduce N/Q/H analysis ... we noticed that the lower case chain letters start to duplicate themselves and are not unique to each segid. when it starts the two letter chain, everything seems unique again. forgive me if that is expected, it just seems kind of strange this was seen in mutlple log files and we are using version Version: 1.8.4 Release tag: 1496 if you need our files or more details, let me know thanks jpd

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ensemble refinement rfree values
by Arjun Raman 19 Dec '13

19 Dec '13

Dear Phenix Guys, I have recently been trying my hand at the ensemble refinement option in phenix.refine. I generally observe an increase in rfree after performing the ensemble refinement with a well refined (using anisotropic B) structure, but the r-free increases are fairly small. For instance, 18.53% to 18.9% (1.8 Angstrom structure) or 20.45% to 21.1% (1.9 A)...I understand what this technically means (the ensemble refined model isn't as good) but given the noise in the calculation due to the limited number of reflections for the test set (~1000), would someone consider these rfree increases significant? My apologies if this question is a well-answered one...I can't seem to find much discussion about the range of rfrees to be expected or whether a 0.3-0.5% increase is large enough to toss out the refinement. Normally, I would take the lower rfree but because the ensemble refinement procedure gives potentially much more information, this seemed like a relevant question to ask. Thanks so much for your time, Arjun Raman Ranganathan Lab UT Southwestern ________________________________ UT Southwestern Medical Center The future of medicine, today.

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MR-SAD, Yb, combined phases
by Joseph Noel 19 Dec '13

19 Dec '13

Hi All, I am carrying out a structure refinement using experimental phases combined with an MR solution. The experimental phases are being determined from bound Yb3+ cations and the data is collected at one of the Yb absorption peaks of 1.385 A. I do have a few questions about the heavy atom arrangement and then refinement. At this wavelength, I am also seeing peaks after running MR-SAD that are actually not the Yb cations but the sulfurs on several of the proteins Cys and Met residues. Should I try and change this "heavy atom arrangement" to include Yb and S before determining the final refined phases that I would like to then use as restraints during the structure refinement? If so, its not clear how to do this in Phenix without it finding additional sites that it attributes to Yb but which are actually sulfurs. For MR, this is an exact structure. All I am doing is using Yb which substitute for Mg coordination sites as a source of experimental phases to see how it improves refinement and maps. Second, when I do refine using the MLHL target function, I am finding quite a bit of excess positive density around the Yb sites. How do I try and account for this? I have attempted to take care of it with ADP and occupancy refinement but that doesn't seem to be enough. The resolution is 2.2 A and the anomalous signal is quite good (alas that is why I am also seeing the sulfurs clearly in the anomalous difference map). Do I need to change the scattering table since the structure now includes at least 4 Yb cations per asymmetric unit (one 550 amino acid residue protein per asymmetric unit - 68% solvent)? Is it important to refine the anomalous groups? For the latter, one can't refine with phase restraints (MLHL) and anomalous groups together. I have to choose one or the other - no phase restraints and anomalous groups refined, or experimental phase restraints and no anomalous group refinement. My goal is to use additional experimental measurements - amplitudes and phases to improve refinement, map interpretation and ultimately ensemble refinement. Any help, comments, criticisms, etc will be very appreciated! Happy Holidays! Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

3 3

phenix.rosetta_refine on OS X?
by Ben Eisenbraun 19 Dec '13

19 Dec '13

4 5

Please apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 16 Dec '13

16 Dec '13

We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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off topic - linux flavors for crystallography
by Todd Jason Green 12 Dec '13

12 Dec '13

Hello All- I have used a trusty box running fedora core 3 for nearly a decade and I am (finally) upgrading to a new workstation. In lieu of Nat's recent mention of new linux installers of phenix, I thought I would try to get a consensus on what linux flavor(s), I should consider installing on my new box. It will be used with emphasis on typical crystallography software including 3D graphics (3 GB NVIDIA Quadro K4000 card). If anyone would like to make a suggestion for an OS, I thank you in advance. Pointers to a web review can work too. Best- Todd

7 7

cyclic peptide refinement
by wei xia 12 Dec '13

12 Dec '13

Hi, I am trying to refine a structure with a cyclic peptide ligand.I create a 'TRANS' link between the C-ter and N-ter residues of the cyclic peptide during refinement.But there is obvious no bond formed between the two residues in the refined structure.I checked the geo file and found that there are only angle restraints but no bond restraints between the two residuesAnyone can help me out?Thanks in advance! Wei P.S. refinement.pdb_interpretation.apply_cif_link { data_link = TRANS residue_selection_1 = chain D and resname MVA and resid 5005 residue_selection_2 = chain D and resname ARG and resid 5001 }

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phenix.find_ncs_from_density density_search.dump_ncs_density doesn't output mtz
by Francis Reyes 11 Dec '13

11 Dec '13

I'd like to see the region of my maps that obey the NCS operators and I was hoping for separate mtz's for each region given I had set density_search.dump_ncs_density = True. However, I'm not getting any output mtzs. Any ideas? Thanks, F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

2 5

phenix.refine nproc
by de Waal, Parker 10 Dec '13

10 Dec '13

Hello Everyone, I recently compiled phenix 1.8.4-1496 on a CentOS 6.4 server and am having trouble using phenix.refine in parallel using the nproc flag which always runs as a single thread. Please find my input parameters here: https://gist.github.com/anonymous/13b9d4d39ed4d0c9622a I'm wondering if maybe OpenMP isn't configured properly on our server? Or maybe the correct version is not installed when I compliled phenix. If anyone has any input or experience with a problem such as this I would be extremely grateful. Cheers, Parker

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Spatial filtering
by Machius, Mischa Christian 06 Dec '13

06 Dec '13

Potentially silly question: is spatial filtering used for increasing contrast in electron density maps? Is it used for any other kind of data manipulation in macromolecular crystallography, e.g., diffraction data processing, density modification, etc. I'm a bit fuzzy on that subject, and so I said 'potentially silly', because it could be that such approaches are totally common but have different names (such as local averaging/scaling and so on). Many thanks in advance. Cheers, MM

2 1

Submissions for next CCN newsletter
by Nigel Moriarty 06 Dec '13

06 Dec '13

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2014 issue is 15 December 2013 but if you can send me an email we can make exceptions so you can use the holiday break to work on your drafts. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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DEN refinement
by Scott Thomas Walsh 05 Dec '13

05 Dec '13

Dear Phenix Users, Is it possible to use NCS restraints in DEN refinement like we can do in regular phenix.refine refinement? Thank you for your help. Cheers, Scott ************************************************ Scott T. R. Walsh, PhD Assistant Professor University of Maryland IBBR/CBMG 3127E CARB-2 9600 Gudelsky Drive Rockville, MD 20850 USA phone: (240) 314-6478 fax: (240) 314-6225 email: swalsh12(a)umd.edu<mailto:[email protected]>

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new Linux installers
by Nathaniel Echols 05 Dec '13

05 Dec '13

Hi Linux/Phenix users-- We are now building installers on several "new" platforms, including Ubuntu 10.04 and several versions of CentOS (which isn't much different from Fedora, except that it's supported by the virtual machine software we're using). Since we don't actually run these OSes outside of the VMs, we're going to crowd-source the testing a little more than usual. Our goal is to retire our ancient Fedora 3 systems - these are old and slow and take up too much space, but it's also the most compatible with other distributions. I'm hoping that the CentOS 5 builds will be a suitable replacement, or perhaps CentOS 4 (but we can only build the 32-bit installer on that OS). In addition to Ubuntu, I'm particularly interested in hearing whether any of these builds runs smoothly on SuSE and Debian. The virtual machine software supposedly supports these OSes too but I haven't yet managed to install SuSE on it after several attempts. The latest builds are here: https://www.phenix-online.org/download/phenix/nightly/?version=dev-1558&sho… We're missing the 64-bit CentOS 5 build right now, but I hope to get that working in the next few days. thanks, Nat

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Re: [phenixbb] reduce hangs
by Andreas Förster 05 Dec '13

05 Dec '13

Dear all, I'm not sure how much of my conversation with Jeff Headd and the comments from others that I received made it onto the mailing list. The problem with reduce being stuck in an infinite loop and refinement never completing has now a workaround, if no solution: Mark van Raaij pointed out that running refinement repeatedly while varying the number of cores would eventually avoid the infinite loop. I didn't observe that, but while running refinement with a handful of Xeons got stuck, running the same job with the same executable on the same OS with a bucketful of Opterons instead succeeded. As I said, there's no solution but a number of ways to get unstuck if you find yourself in the same situation like Mark and me. Best. Andreas -------- Original Message -------- Subject: Re: [phenixbb] reduce hangs Date: Wed, 4 Dec 2013 09:46:20 -0500 From: Jeff Headd <jjheadd(a)lbl.gov> To: Andreas Förster <docandreas(a)gmail.com> If the different machine is a slightly different architecture it's possible that it may run, even under the same OS version. My guess is that it's down to slight floating point differences in the coordinates throughout the course of refinement, but it's so hard to pinpoint. If you have access to other machines it is probably worth trying. <snip> Jeff

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Coot not allowing real space refinement when connected to phenix
by Jobichen Chacko 05 Dec '13

05 Dec '13

Dear All, I recently upgraded to latest version of coot (version0.7.2). When I try to do the Real space refine zone option, coot is giving the following complaint (Refinement setup failure. Failed to find restraints for PROLYSILE). But it works fine when I open coot separately from a terminal and read the pdb and mtz file. I downloaded this coot along with the ccp4 package and it also works fine when I open from ccp4 interface. Any suggestions will be much appreciated. Jobi

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hi.
by Hexi Zhang 04 Dec '13

04 Dec '13

http://satis.egitmeni.org/dxibo/axzjmylquusc.html Hexi Zhang

1 0

reduce hangs
by Andreas Förster 03 Dec '13

03 Dec '13

Dear all, I'm refining a structure with 11 molecules in the asymmetric unit. Recently I took out NCS (data are to 2.2A and differences between molecules of interest). Refinement now stalls halfway through with two reduce jobs running at 100% CPU. The current job has been sitting like this for four days. The last entry in the log file are a few XYZ individual lines. Refinement includes XYZ, TLS, individual B, weight optimization. I launched 8 cycles. Phenix hangs after 4_bss. I've observed this twice in a row. Any suggestions to overcome this, short of going back to using NCS? This is with Phenix dev-1538 on RHEL 6.3. Thanks. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London

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AutoSol/Heavy atom sites/outside the model
by Egor Tchesnokov 03 Dec '13

03 Dec '13

Thank you for the feedback. WinCoot 0.7/Draw/Cell Symmetry brings up "Show Symmetry" window, which only allows to alter the display but not to coincide the heavy atom sites with the model. Am I not looking at the right menu in Coot ? Thank you for your time and help. Egor

1 0

Autobuild combine
by Heather L Condurso 02 Dec '13

02 Dec '13

Hi all, I am still having issues with Autobuild giving errors during the combine step. I've downloaded the latest build and hope that will solve the problem, but in the mean time I'm having an issue trying to combine the models. I've been following the script: #!/bin/csh -f #COMBINE_MODELS SCRIPT if (-d PDS || -d AutoBuild_run_1_) then echo "Please run in a directory without PDS or AutoBuild_run_1_" exit 1 endif echo "Setting up combine models with a dummy run. NOTE: multiple_models_group_number must be correct" phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat combine_only=true multiple_models_group_number=2 multiple_models_number=1 > dummy_autobuild.log echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS" mkdir AutoBuild_run_1_/MULTIPLE_MODELS cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp map_coeffs_1.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1 cp map_coeffs_2.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2 ls AutoBuild_run_1_/MULTIPLE_MODELS/ echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS" phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 > autobuild_combine.log # END OF COMBINE_MODELS SCRIPT # Here are the two log files. I used the expl_fobs_phases_freeR_flags.mtz as fobs.mtz and changed each overall_best.pdb and overall_best_refine_map_coeffs.mtz as the model and map to combine. Thanks, Heather

2 2

AutoSol/Heavy atom sites/outside the model
by Egor Tchesnokov 02 Dec '13

02 Dec '13

Hello, Level: beginner 1. Data collected at wavelength of 0.9537 2. Ran Xtriage: anomalous data seem to extend to 2.2 A 3. Ran Phaser-MR to get partial model (1 copy in AU) 4. Ran AutoSol using partial model and anomalous data AutoSol finds heavy atom sites (FOM=0.69; Overall score=75.6+/-3.3). Coot displays model/density without heavy atoms Heavy atoms are displayed outside the model (using zoom out). Question: what did I do wrong? Thank you for your time and help. Egor

2 1

Red patches of electron density
by Singh, Bishal 02 Dec '13

02 Dec '13

Hi, I am solving a crystal structure at 1.2 Å with completeness 97.3% in the highest resolution shell. There are few small patches of red electron densities on the main chain of a flexible loop at a contour level of ~3sigma of difference ED map. Refinement parameters were following: XYZ coordinates, individual B-factor, optimize X-ray/stereochemistry weight, optimize X-ray/ADP weight and individual Anisotropic ADP for amino acids excluding hydrogen. Target weights are as default in phenix.refine. I already have observed two alternative conformation for this region in another crystal structure. Therefore I am thinking that these red patches are because of lower occupancy of these residues. Please suggest me what shall I do. I shall be grateful for your words. With regards, Bishal Singh University of Heidelberg, Germany

2 1

Iterative build omit map error
by Heather L Condurso 27 Nov '13

27 Nov '13

SO just as my omit map run should have finished, it gave an error instead. I'm running 1.8.4-1496 on a Mac with OSX 10.6.8 and 8GB of memory. Here is the end of the log file: Splitting work into 32 jobs and running with 1 processors using sh background=False in /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_3.log Starting job 4...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_4.log Starting job 5...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_5.log Starting job 6...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_6.log Starting job 7...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_7.log Starting job 8...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_8.log Starting job 9...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_9.log Starting job 10...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_10.log Starting job 11...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_11.log Starting job 12...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_12.log Starting job 13...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_13.log Starting job 14...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_14.log Starting job 15...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_15.log Starting job 16...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_16.log Starting job 17...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_17.log Starting job 18...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_18.log Starting job 19...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_19.log Starting job 20...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_20.log Starting job 21...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_21.log Starting job 22...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_22.log Starting job 23...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_23.log Starting job 24...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_24.log Starting job 25...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_25.log Starting job 26...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_26.log Starting job 27...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_27.log Starting job 28...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_28.log Starting job 29...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_29.log Starting job 30...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_30.log Starting job 31...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_31.log Starting job 32...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log : /TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz Rebuilding side chains from Build_composite_refined_3.pdb Refining model: edit_model.pdb approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.0197876048373 approx_equal ERROR 0.0197856373852 approx_equal ERROR Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log : /TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz Rebuilding side chains from Build_composite_refined_3.pdb Refining model: edit_model.pdb approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.0197876048373 approx_equal ERROR 0.0197856373852 approx_equal ERROR Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz ******************************************************************************** Can this be salvaged? It took 5 days to run. I found a section about this in the documentation, but I can't find the maps for each region overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. I can only find working_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. Will these maps work? Can you tell what the error means so that I can avoid this problem in the future? Thanks, Heather

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zero B-factors
by Edna Patricia Matta, Ms 26 Nov '13

26 Nov '13

Hello, Recently I did submit a structure to the PDB but they found that some atoms had zero value for the B-factors. I am new in this filed and I do not know what to do. There have been reports of problems with some versions of phenix about this. I used Phenix 1.8. I repeted the refinement doing restrain NCS-related B-factors but I do not find where to check for the the B-factor values in the the log file. Somebody can help me? Thanks a lot, Edna

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Re: [phenixbb] [ccp4bb] Ligandfit - problem with ligand_start
by Terwilliger, Thomas C 25 Nov '13

25 Nov '13

Hi Danilo, The most likely problem is that the ligand_start file has to have enough atoms in it to define a fixed group in the ligand. The way that ligandfit works is that it breaks a ligand up into rigid groups connected by rotatable bonds. The ligand_start file has to contain one complete rigid group. So probably if you supply a little more of the ligand then it might run. Just to test this, can you try this test of using a ligand_start file: phenix_regression.wizards.test_resolve resolve test_fit_start And then if that gives an "OK", try this: cd test_fit_start phenix.ligandfit ligand=side.pdb ligand_start=start.pdb resolve_map.mtz quick=true Does that run? If you the look at LigandFit_run_1_/TEMP0/resolve_ligand_fit.log Does that say >ligand_start start.pdb Starting configuration of ligand will be read from: start.pdb If all that works, then try adding more atoms to your ligand_start file. Let me know if that doesn't do it! All the best, Tom T Dear all, I am working on a membrane protein covalently bound to a molecular antanna: it is known that this molecule binds to lysine residue but I do not know how many and which lysine residues it binds. 20 diffraction datasets of this protein-ligand complex have been obtained and now, I would quickly localize the ligand using the Fo-Fc map of each data set and using the information on the covalent bound protein-ligand. Ligandfit tool (PHENIX) seems to be indicated to do this; to use the information on the covalent bound, I am using the ligand_start keyword with a pdb containing a ghost atom (however present in ligand model) perfectly superposed to the lysine atom that should bind the ligand. The command used is: phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \ refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif description: - prot.mtz (data) - prot.pdb (protein without ligand) - lig.pdb (ligand containing ghost atom) - lig_start.pdb (ghost atom superpose to NZ of a lysine) - lig.cif (restrain of lig.pdb) Strangely, no ligand is found at the end of the process even reducing ligand_cc_min to 0.01. I have run the same command by using an other protein where an other ligand has been correctly fitted but, also in this case, no ligand has been detected. Conversely, without the use of ligand_start, ligandfit properly localizes the ligand. I'm doing some mistake in the use of ligand_start? Do you know an other tool to perform a ligand fitting in these conditions? Thanks for your answers. Danilo

1 0

Ligandfit - problem with ligand_start
by Danilo Belviso 25 Nov '13

25 Nov '13

Dear all, I am working on a membrane protein bound to a antenna molecule: I know that the molecule binds to lysine residue but I do not know how many and which lysine residues it binds. 20 diffraction datasets of protein-ligand complex have been obtained and now, I would quickly localize the ligand using the Fo-Fc map of each data set and using the information on the covalent bound protein-ligand. Ligandfit tool (PHENIX) seems to be indicated to do this; to use the information on the covalent bound, I have thought to use the ligand_start keyword with a pdb containing a ghost atom (however present in ligand model) perfectly superposed to the lysine atom that should bind the ligand. The command used is: phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \ refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif description: - prot.mtz (data) - prot.pdb (protein without ligand) - lig.pdb (ligand containing ghost atom) - lig_start.pdb (ghost atom superpose to NZ of a lysine) - lig.cif (restrain of lig.pdb) At the end of the processing, ligand is not found. So, I have tryed with ligand_cc_min=0.01, but also in this case ligandfit does not give result. I have thought that no ligand is present. However, to be sure that all was correct, I have run the same command by using an other protein where an other ligand has been correctly fitted. Also in this case, no result has been obtained. Conversely, without the use of ligand_start, ligandfit properly localizes the ligand. I'm doing some mistake in the use of ligand_start? Thanks for your answers. Danilo

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