- phenixbb - phenix-online.org

sequence independent model building possible?
by Kaushik Hatti 06 Feb '16

06 Feb '16

Hello, Is abinitio model building possible for a map with poly alanine model at 1.9A resolution? We thought we had crystallised our protein of interest X, collected data at 1.9 A and all attempts to solve protein X (which has many homologs) through MR failed. All attempts to re-crystallise the same protein also failed. Now, we think the initial protein which got crystallised could be a contaminant (we don't have any crystals left from this batch to check for the sequence of the crystallised protein). Through various methods (and a bit of luck) we have arrived at a decent map with LLG : 3600 and TFZ: 22 and R/Rfree : 37/41 (for a poly alanine model). I believe these scores indicate right fold. As I still don't know the sequence information, is it possible to build sidechains directly from the map (I could only identify a couple of residues and the model largely remains PolyAla)? Autobuild with Rebuild-in-place didn't help in identifying any more residues. I have also searched PDB database for similar structures. But, none of those are either from our expression system (E. coli) or organism of our protein of interest. Neither did I find any similar sequences from E. coli or our organism of interest. Any leads/suggestions would be helpful. Thanks, Kaushik, MRN Murthy lab, MBU, IISc, India -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

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scaling in Fo-Fo maps
by Xun Lu 04 Feb '16

04 Feb '16

Hello everyone, I have a question on how the scaling is done when generating Fo-Fo maps in Phenix. So I want to compare three datasets (of the same protein of course): A,B,C. I generated three maps: A-B, A-C, B-C, and I can see the differences. But I also want to compare the peaks in the three maps, so I want to make sure the maps are generated using the same scaling. Thanks, Xun p.s. Any other ideas to compare three datasets?

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Feature enhanced map with twinned data
by Matthias Uthoff 04 Feb '16

04 Feb '16

Hi all, I am processing the data of a twinned crystal (fraction approx. 40%) and I was wondering if the FEM module as implemented in Phenix can cope with twinned data? Or should I use a detwinned dataset? Best regards, Matthias -- Matthias Uthoff, PhD Student Institute for Biochemistry University of Cologne Otto-Fischer-Str. 12-14 D-50674 Cologne Phone: +49 221 470 3211 E-Mail: matthias.uthoff(a)uni-koeln.de Internet: http://px.uni-koeln.de

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CORRECTION: refinement of peptide links in mmcif coordinates (multi character chain identifiers)
by wtempel 03 Feb '16

03 Feb '16

Hello all, thanks to Nigel Moriarty, I realized that the problem I encountered had nothing to do with PHENIX, but everything with less-than-careful analysis on my part. The relevant peptide bonds do in fact appear well-restrained by PHENIX. I apologize for the confusion. Wolfram

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refinement of peptide links in mmcif coordinates (multi character chain identifiers)
by wtempel 03 Feb '16

03 Feb '16

Dear PHENIX users, for a structure with approx. 30 instances of an N-terminal AYA (N-acetylalanyl) residue, I have noticed that PHENIX did not restrain planarity of the peptide bond with the next residue. What is the recommended way of restraining those peptide bonds' dihedral angles and bond distances? Thank you, Wolfram Tempel

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Rosetta refine
by Nigel Moriarty 02 Feb '16

02 Feb '16

Folks There has been a problem with the interface between Phenix and Rosetta when running phenix.rosetta_refine due to the randomness involved in the models created by Rosetta. We (mostly Frank DiMaio) have tracked and corrected it. After two weeks of testing, I feel comfortable recommending that users move to 2016.02.58402 bundle. This version update relates only to Rosetta refinement. If you are only using MR Rosetta or ERRASER you may continue using the previous versions. If you wish to use (or even hope to use) programs from both piles, you can follow the installation notes for Rosetta refinement and simply point your environmental variables used (which are common to all three programs) to the new bundle. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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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Problems installing 1.10.1 on RHEL 6.3
by David Briggs 02 Feb '16

02 Feb '16

Hi Phenix, We are trying to upgrade Phenix on our Linux box running RHEL 6.3, kernel 2.6.32-279.14.1.el6.x86_64. I have attempted to install the Centos 5 build and I get an error message during installation: Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/public/packages/phenix-1.10.1-2155/base/bin/python /home/public/packages/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/public/packages/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code -11 When I attempt install the CentOS6 build I can install Phenix, but when I try and launch it I get a different error message: Traceback (most recent call last): File "/home/public/packages/phenix-1.10.1-2155/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/home/public/packages/phenix-1.10.1-2155/build/../modules/phenix/wxGUI2/command_line/main.py", line 16, in run from wxGUI2 import App File "/home/public/packages/phenix-1.10.1-2155/modules/phenix/wxGUI2/App.py", line 15, in <module> import wx File "/home/public/packages/phenix-1.10.1-2155/base/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module> from wx._core import * File "/home/public/packages/phenix-1.10.1-2155/base/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module> import _core_ ImportError: /home/public/packages/phenix-1.10.1-2155/base/bin/../lib/libXrender.so.1: undefined symbol: _XGetRequest Should I give up and attempt to compile from the source, or is there a fix for these issues? Kind regards, Dave -- -- David Briggs about.me/david_briggs

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Nvidia Quadro M4000 for Coot 3D?
by Xiao Lei 01 Feb '16

01 Feb '16

Hi All, As I read the Coot 3D setting guide online, it says for Linux environment I have to have at least a Nvidia Quadro card with 3 pin min DIN stereo connector and DVI connector, and the cheapest is Nvidia Quadro K4200. I plan to buy Dell workstations for Coot 3D, but they do not have the option of Quadro K4200, instead, they suggests an updated version called Quadro M4000. As I look at the product picture of Quadro M4000, I can see all connectors are DPs (displayport), not DVI connector. What is more, the Quadro M4000 does not have any connector for 3 pin mini DIN. Is the Quadro M4000 card still suitable for Coot 3D in Linux? Do I have to manually add a 3 Pin Mini DIN Bracket Stereo Connector to the Quadro M4000 card (which can be found at B&H photos) and get a Displayport to DVI connectors before it works? In addition, I found it was very hard to find a new build-in IR emitter 3D monitor from Asus or Acer, so I am looking for a Asus 3D monitor with Nvidia 3D vision 2 kits, some pictures of the 3D vision 2 kit only shows USB cable as connectors, I wonder if the kit also contains a 3-pin min din cable for the 3D? I'd appreciate if any input on this.

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new opening for Scientist 1, Structural Biology at Plexxikon Inc. (Berkeley, CA, USA)
by Ying Zhang 01 Feb '16

01 Feb '16

Dear all, This post is to bring your attention to a job opportunity for crystallographer at Plexxikon Inc. Plexxikon is a leader in the discovery and development of novel, small molecule pharmaceuticals. The company has utilized its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage programs in a number of therapeutic areas. Plexxikon's most advanced program, Zelboraf(r) (vemurafenib, and formerly known as PLX4032), was approved by the FDA in 2011 and is approved in over 60 countries worldwide. Plexxikon's demonstrated capability in discovery and early development uniquely positions the company to develop multiple commercial franchises for different therapeutic indications, and create significant value for Plexxikon and its collaborators. Plexxikon's novel discovery approach, combined with an experienced management and scientific team, a broad network of scientific and clinical experts, and partnerships that support later stage development, have been key drivers of the company's success since it began operations in 2001. In April 2011, Plexxikon became a member of the Daiichi Sankyo Group, and continues to build its broad and diverse pipeline and R&D operations independently. Plexxikon is a small business with less than 75 employees and this position will be a critical member of the Structural Biology team reporting to an experienced scientist. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. For job responsibilities and Position requirements, please see the following website. http://careers.jobscore.com/jobs2/plexxikon/scientist-1-structural-biology/… If you are interested, please directly apply through the above link. Please don't reply to this email. Best Regards, Ying Zhang Sr. Scientist Plexxikon Inc.

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Macromolecular Crystallography School 2016 (Madrid, Spain)
by Pavel Afonine 01 Feb '16

01 Feb '16

Dear colleagues, on behalf of the organizers (Armando Albert, Juan Hermoso and Isabel Usón): announcement of the 7th edition of the Macromolecular Crystallography School in Madrid. Please direct all questions regarding the School to the organizers. ****** Dear colleagues, We are pleased to announce the Seventh edition of the Macromolecular Crystallography School 2016, to be held at the Institute Química-Física Rocasolano- CSIC (Madrid, Spain). Dates: May 25 - 29, 2016 Invited speakers and tutors: Paul Adams, Berkeley, USA Pavel Afonine, Berkeley, USA Armando Albert, Madrid, Spain Kay Diederichs, Konstanz, Germany Paul Emsley, Cambridge, UK Carmelo Giacovazzo, Bari, Italy Xavier Gomis-Ruth, Barcelona, Spain Juan Hermoso, Madrid, Spain Eugene Krissinel, Oxford, UK Rob Nicholls, Cambridge, UK Maria Solá, Barcelona, Spain Isabel Usón, Barcelona, Spain Please find the program of the Workshop, the application form and further information, at http://www.xtal.iqfr.csic.es/MCS2016/ Applicants: The workshop has been designed for postgraduate, postdoctoral and research scientists that deal with macromolecular crystallography but need further knowledge on the routine uses, the state of the art and fundamentals that underlie the modern techniques for macromolecular crystallography. The topics will cover crystallographic computing and fundamentals using XDS, CCP4 and Phenix, as well as the state of the art on topics such as the strategies for protein production, phasing with ARCCIMBOLDO, SHELX and SIR2014, modeling with COOT and low resolution techniques. MCS2016 will provide five days of lectures and workshops. The course is designed for 25 highly motivated students. Requests to participate must be sent by a free-formated E-mail, before March 28, 2016 to the following address: cursos(a)fgua.es <mailto:[email protected]>, indicating the motivation to participate and experience on macromolecular crystallography and including a letter of recommendation from PhD Director (only for PhD students). Accepted participants will be notified by e-mail before April 4, 2016. Organizers: Armando Albert (xalbert(a)iqfr.csic.es <mailto:[email protected]> ), Juan Hermoso (xjuan(a)iqfr.csic.es <mailto:[email protected]>) and Isabel Usón (iufcri(a)ibmb.csic.es <mailto:[email protected]>) ****** Pavel

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ACA 2016 SAS Workshop
by Kushol Gupta 01 Feb '16

01 Feb '16

On behalf of the organizing committee, I am pleased to announce a workshop on "Computational Approaches to the Structural Modelling of Biological Macromolecules using Small Angle Scattering." This workshop will take place on Friday, July 22nd, 2016 at this year's American Crystallographic Association (ACA) Meeting in Denver, Colorado, U.S.A. The meeting itself will run from July 22-26. WK.02 Computational Approaches to the Structural Modelling of Biological Macromolecules using Small-Angle Scattering. This one-day workshop will focus on computational approaches to structural modelling and analysis. In the first session, a brief reprise of fundamental concepts will be provided, with a focus on pitfalls in data acquisition and reduction that can affect subsequent data analysis and modelling. The remainder of the day will be allocated to the hand-on application of the leading software packages to the analysis of solution scatter. This workshop will feature direct participation from the creators of the most prevalent software packages currently used (including BIOSAXS(EMBL), SIBYLS, CCP-SAS, FoXs and IMP). The participating groups will present their software, including the basis for the algorithms employed, and further deliver guided hands-on tutorials for workshop participants. This approach will introduce and train participants on the appropriate application of these tools, including experimental design, model preparation, comparison of structural models using both SAS and complementary information, validation, and most importantly the limitations of interpretation with regards to the biological conclusions that can be made. The workshop format will include lectures, and a selection of hands-on practical exercises. Students will be expected to bring laptops with appropriate pre-installed software as necessary. Prior to the workshop, a website will be made available containing installation instructions and software for each tutorial. Tentative Program Schedule Basic Theory and Methods Joint Session 8:00 am - 9:30am - Introduction: what is SAS data good for? (short) - Theory Essentials: How to get your scattering profiles - SAXS and SANS: common pitfalls, how to ensure the data is suitable for modelling - Cross Checks and Validation 9:30 AM - 10:00 AM Coffee Break Software Application and Tutorial Session 10 am - 7pm 10:00 AM - 11:30 AM BIOSAXS(EMBL) lectures and guided tutorial 11:30 AM - 12:30 PM Lunch and Discussions (vendor presentations in the form of 'lunch and learn') 12:30 PM - 2:00 PM IMP Lectures and Guided Tutorial 2:30 PM - 3:00 PM Coffee Break 3:00 PM - 4:30 PM SIBYLS lectures and guided tutorial 4:30 PM - 6:00 PM CCP-SAS lectures and guided tutorial 6:00 PM - 7:00 PM Discussion Pre-registration is mandatory. The fee to attend is: . Student (undergrad, grad or postdoctoral) - $140 . Corporate - $275 . Non corporate or non student - $140 Lunch will be included. Organizers: . Angela Criswell Rigaku Americas Corporatio Angela.Criswell(a)rigaku.com . Richard Gillilan Cornell CHESS reg8(a)cornell.edu . Kushol Gupta Perelman School of Medicine, University of Pennsylvania kgupta(a)upenn.edu . Michal Hammel SIBYLS group at The Advanced Light Source (ALS) mhammel(a)lbl.gov . Susan Krueger NIST Center for Neutron Research/CCP-SAS susan.krueger(a)nist.gov . Maxim Petoukhov BIOSAXS group at the European Molecular Biology Laboratory (EMBL) maxim.petoukhov(a)embl-hamburg.de . Adam Round EMBL Grenoble around(a)embl.fr . Dina Schneidman Institute of Life Science, Hebrew University of Jerusalem dina.schneidman(a)mail.huji.ac.il . Jill Trewhella University of Sydney jill.trewhella(a)sydney.edu.au More information is available at: http://www.amercrystalassn.org/wk.02-saxs http://www.amercrystalassn.org/2016-meeting-homepage Kushol Gupta, Ph.D. Research Assistant Professor Department of Biochemistry and Biophysics Perelman School of Medicine at The University of Pennsylvania <mailto:[email protected]> kgupta(a)upenn.edu / 215.573.7260 / 267.259.0082 / <http://www.stwing.upenn.edu/~kgupta> www.stwing.upenn.edu/~kgupta

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Additional conformations and partially occupied waters
by Helena Taberman 31 Jan '16

31 Jan '16

Hi, I’m trying to refine a structure determined to 1.6 Å resolution. There’s several residues with additional conformations and waters with partial occupancies stating that they would be there when the conformation of the residues allows it. When I try to refine these conformations and partially occupied waters together the refinement kicks the second conformations and water molecules out of their densities, since they are obviously too close to the other additional conformations of the residues or the following residues. What could I do? Should I somehow group them together or what? Best regards, Helena Helena Taberman, Ph.D. University of Eastern Finland Department of Chemistry Joensuu Campus P.O. Box 111 FI-80101 Joensuu, FINLAND Mobile: +358 50 337 2488

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Phenix Refine Place Elemental Ions
by Xiao Lei 30 Jan '16

30 Jan '16

Hi Phenixbb members, I have a dataset of 2.7A resolution and solved by molecular replacement. Now I am refining my structure using Phenix Refine (Fedora; Version 1.10.1). I'd like to try "place elemental ions" option in the GUI. I read the Phenix refine manual and it says: " to enable this option, simply enter a list of the elements to search for; this will also enable solvent picking as a first step. This option is not recommended if you have data worse than 3.0A resolution, and works best with anomalous data." I have questions about this: 1. In my crystallization condition I have 80 mM CaCl2 and 5mM MgCl2. How should I enter the ions to search for into the GUI? Should I enter "Ca; Mg" or "Ca and Mg" or "Calcium and Magnesium" ? I wonder how the Phenix Refine can really differentiate Ca or Mg in the map. 2. Phenix Refine says the place elemental ion option works best with anomalous data, does the anomalous completeness needs to be over 80% to consider anomalous data? Tough I did not do MIR or Selenium which produces anomalous signals for phase, Phenix Xtriage shows my data has anomalous completeness around 70% (I even do not know what caused the anomalous signal in my dataset). Does this help Phenix Refine to locate elemental ions? Thanks ahead.

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American Crystallographic Association Annual Meeting - Call for papers
by Terwilliger, Thomas Charles 29 Jan '16

29 Jan '16

Hi Phenix colleagues! Here is the announcement of the American Crystallographic Association 2016 Annual Meeting July 22 - 26 in Denver, Colorado! All the best, Tom T Tom Terwilliger 2016 ACA President Call for Papers for the American Crystallographic Association 2016 Annual Meeting July 22 - 26 in Denver, Colorado Web site: http://www.amercrystalassn.org/2016-meeting-homepage Abstract deadline is March 31 * Exciting sessions highlighting structural dynamics, sessions on sources, methods, and results. These include opportunities from new and improved instrumentation, single/multiple crystal, powder and solution methods, and hot structural results. * Full scientific program at www.amercrystalassn.org/2016-meeting-homepage * Sessions for young scientists on career directions, reviewer practices and more * Lower registration fees for members * No abstract submission fee * Travel funding for young scientists * 40% of all talks chosen from contributed abstracts * Held at the Denver Sheraton, in the heart of the city * Special, reduced hotel rates for Students & Postdocs Links to the meeting: Registration: http://www.amercrystalassn.org/2016-registration Students: http://www.amercrystalassn.org/2016-mtg-student-page Membership: http://www.amercrystalassn.org/content/pages/main_membership Exhibit show: http://www.amercrystalassn.org/2016-exhibit-show Deadlines: http://www.amercrystalassn.org/2016-meeting-homepage Awards: http://www.amercrystalassn.org/2016-award-winners Young Scientists: http://www.amercrystalassn.org/2016-mtg-student-page ACA Home page: http://www.facebook.com/AmerCrystalAssn ACA mailing address: ACA, POBox 96 Ellicott Station Buffalo, NY 14205-0096 ACA Email: aca(a)hwi.buffalo.edu

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No Sigmas in Phenix Refinement?
by Keller, Jacob 29 Jan '16

29 Jan '16

Dear Phenix Team, I heard a rumor that Phenix does not use experimental sigmas in refinement--is this true? JPK

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Re: [phenixbb] ligand modification / combination in REEL
by andre.stiel 28 Jan '16

28 Jan '16

Nigel, crazy thing, I repeated the ELBOW run with the exact same smiles for: 1.10-2155 and 1.10.1-2155 and it gives different results. With the newer version addressing the sugar correctly, as you said. Thanks! André André C. Stiel, Ph.D. (PI) +49 (0) 89 3187 3972 Office: Building 57, Room 009 Cell Engineering Group Institute of Biological and Medical Imaging > Am 21.01.2016 um 19:12 schrieb Nigel Moriarty <nwmoriarty(a)lbl.gov>: > > Andre > > I note that you use 1.10-2155. It works correctly with the latest nightly build. You could also try 1.10.1-2155 if you are more comfortable with major releases. Version 1.10-2155 was replaced with 1.10.1-2155. > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 33R0349, 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 <http://cci.lbl.gov/> > On Wed, Jan 20, 2016 at 11:51 PM, andre.stiel <andre.stiel(a)helmholtz-muenchen.de <mailto:[email protected]>> wrote: > Hi Nigel, > thanks for your time, here you go. And I attached the .cif I obtain from ELBOW > > Helmholtz Zentrum Muenchen > Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) > Ingolstaedter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de <http://www.helmholtz-muenchen.de/> > Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe > Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) > Registergericht: Amtsgericht Muenchen HRB 6466 > USt-IdNr: DE 129521671 > > > > http://www.chemspider.com/Chemical-Structure.28639235.html?rid=ac73301e-ee9… <http://www.chemspider.com/Chemical-Structure.28639235.html?rid=ac73301e-ee9…> > CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O[C@@H]1[C@@H]([C@@H]([C@H]([C@@H]([C@H]1O)O)O)O)O)OC(=O)CCCCCCC/C=C\C/C=C\CCCCC > > cheers > André > > >> Am 20.01.2016 um 21:40 schrieb Nigel Moriarty <nwmoriarty(a)lbl.gov <mailto:[email protected]>>: >> >> Its is very strange that the SMILES string is resulting in an aromatic ring. Can you send me the SMILES? >> >> Cheers >> >> Nigel >> >> --- >> Nigel W. Moriarty >> Building 33R0349, Physical Biosciences Division >> Lawrence Berkeley National Laboratory >> Berkeley, CA 94720-8235 >> Phone : 510-486-5709 <tel:510-486-5709> Email : NWMoriarty(a)LBL.gov <mailto:[email protected]> >> Fax : 510-486-5909 <tel:510-486-5909> Web : CCI.LBL.gov <http://cci.lbl.gov/> >> On Sat, Jan 9, 2016 at 3:38 AM, andre.stiel <andre.stiel(a)helmholtz-muenchen.de <mailto:[email protected]>> wrote: >> Hi, >> >> I have a phosphatidyl inositol ligand without an existing CIF file only smiles. When I construct the ligand from the smiles ELBOW regards the sugar as just an aromatic ring. >> So I see three possibilities how to end up with a proper constraints file for my ligand (that is: tails like in the smiles but with a proper sugar (chair) conformation on top): >> 1. Can I edit the aromatic ring in REEL in a way to push it into the desired boat/chair conformation? I did not find a command to that end although he can clearly „see“ this conformation as I know from another ligand. >> 2. Can I chop the sugar part from the .CIF of another ligand and somehow fuse it to my tails? >> 3. There is a sugar editor in REEL (which however crashes at the moment for me (Version 1-10-2155)) can I use this to construct the desired sugar and somehow fuse it to the rest… basically like option 2? >> I have not found a very extensive documentation on how to play such tricks with REEL. >> Or would I have to rebuild a complete ligand with this SCALES? >> >> Other suggestion how to get my ligand are also welcome. >> >> Thanks >> >> André >> >> Helmholtz Zentrum Muenchen >> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) >> Ingolstaedter Landstr. 1 >> 85764 Neuherberg >> www.helmholtz-muenchen.de <http://www.helmholtz-muenchen.de/> >> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe >> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) >> Registergericht: Amtsgericht Muenchen HRB 6466 >> USt-IdNr: DE 129521671 >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb> >> Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> > > > Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

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7th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 27 Jan '16

27 Jan '16

First announcement 7th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. May 16 - May 20, 2016 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/15 Application deadline: April 1, 2016 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 1, 2016. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Faculty Positions in Structural Biology at Purdue University
by Noinaj, Nicholas 26 Jan '16

26 Jan '16

PHENIXbb, I wanted to bring to your attention that our Structural Biology group here at Purdue University is looking to hire three new faculty members at the Assistant (tenure-track), Associate, and Full Professor ranks, as outlined in the job ad. The official ad from Science can be accessed via this link (copied below as well): http://jobs.sciencecareers.org/job/391248/faculty-positions-in-structural-b… It is important to also add that Purdue University has just made a HUGE investment of more than $250 million to life sciences over the next five years to advance research. http://www.purdue.edu/newsroom/releases/2016/Q1/purdue-to-invest-more-than-… As a new faculty member myself, I can attest that Purdue is an amazing place to do research! We have all the resources needed to do cutting-edge studies in structural biology on many types of projects including drug discovery, enzymes, viruses, protein assemblies and complexes, membrane proteins, and more. Please forward this email to others who may be interested and/or actively looking for a faculty position, but not on PHENIXbb or CCP4bb. Thanks in advance! Cheers, Nick ------------------------------- Nicholas Noinaj 240 S. Martin Jischke Dr. Hockmeyer Building of Structural Biology, Rm 333 Dept. of Biological Sciences, Purdue Univ. West Lafayette, IN 47907 765-496-0061 (office) 765-496-0059 (wetlab) +++++++++++++++++ Faculty Positions in Structural Biology Markey Center for Structural Biology Department of Biological Sciences The Department of Biological Sciences, Purdue University, is initiating a major effort to expand its investment in Structural Biology and invites applicants at all academic professorial levels to fill multiple new tenure-track faculty positions in this accelerating area. The Structural Biology Group at Purdue is recognized worldwide for its leadership in structural biology of viruses, membrane proteins, and technical approaches to crystallographic and electron microscopy challenges. Creative investigators in a variety of research approaches, X-ray crystallography, NMR spectroscopy and electron microscopy, are sought to enhance these current structural investigations. Potential areas of research interest include but are not limited to studies of viruses and other pathogens, membrane proteins, cancer biology, target molecules for structure-based drug discovery and development of new technologies in structural biology. This position is aligned with major campus-wide investments in the life sciences including the Center for Drug Discovery (https://www.purdue.edu/research/pcdd/), the Center for Integrative Neurosciences and the Institute for Inflammation, Immunology and Infectious Disease (https://www.purdue.edu/research/life-sciences/). Applicants for senior positions in Structural Biology must have a Ph.D. or equivalent in an appropriate discipline and currently hold a position equivalent to an Associate or Full Professor. Structural biologists with a clear cancer focus in their research will also be considered by the Purdue Center for Cancer Research as a Walther Cancer Professor (https://www.cancerresearch.purdue.edu). Applicants at the junior rank in Structural Biology must have a Ph.D. or equivalent in an appropriate discipline and at least 2 years of postdoctoral experience. There is particular interest in researchers trained in single particle cryo-electron microscopy or whole cell electron tomography. Successful applicants for these positions are expected to direct a dynamic and collaborative research program in structural biology to address fundamental questions in the area of human disease, to excel at teaching at the undergraduate and/or graduate level and participate in ongoing programs at Purdue. Extensive opportunities for collaboration exist within the Department, which has over 50 faculty members conducting research in neurobiology, virology, microbiology, molecular and cell biology, bioinformatics, evolutionary biology and ecology (http://www.bio.purdue.edu/). These opportunities are enhanced by a highly interactive community of scientists within the Colleges of Science, Pharmacy, Veterinary Medicine and Engineering and existing and emerging interdisciplinary centers in the life sciences. Abundant infrastructure support for structural biology exists, including advanced imaging analysis and biophysical instrumentation available in established core facilities at the Bindley Bioscience Center and the Birck Nanotechnology Center in Discovery Park (http://www.purdue.edu/discoverypark/). Applications should be submitted electronically to https://hiring.science.purdue.edu/ as a single PDF file containing a letter of interest, a detailed curriculum vitae, contact information for three references, a two to three page summary of research interests, and a one-page teaching statement. The Department of Biological Sciences is committed to advancing diversity in all areas of faculty effort - scholarship, instruction and engagement. Candidates should address at least one of these areas in their cover letter, including past experience, current activity and/or future goals to promote a climate that values diversity and inclusion. As an ADVANCE institution, Purdue University is dedicated to the recruitment, retention and advancement of women in the STEM disciplines. Inquiries should be directed to Cynthia Stauffacher, Chair, Structural Biology Search Committee StructureSearch(a)bio.purdue.edu<mailto:[email protected]> Structural Biology Search Committee Department of Biological Sciences Purdue University, 915 W. State St., West Lafayette, IN 47907-2054. Review of applications will begin December 15, 2015 and continue until these positions are filled. A background check is required for employment in this position. Purdue University is an EOE/Affirmative Action Employer. All qualified applicants, including minorities, women, individuals with disabilities and veterans are encouraged to apply. +++++++

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postdoctoral position MRC Laboratory of Molecular Biology
by Roger Williams 26 Jan '16

26 Jan '16

A three-year postdoctoral position is available with the group of Roger Williams at the MRC Laboratory of Molecular Biology in Cambridge, UK. The project, which is funded by Cancer Research UK is aimed at understanding structural mechanisms of regulation of the target of rapamycin complexes. Specifically to undertake research to investigate the structures and regulation of the mTORC1 complex assembled with its regulators on lysosomal membranes. The objective is to determine the structures of mTORC1 in complexes with its regulators and to understand how these complexes assemble on lysosomal membranes. Methods involved in the study include large scale mammalian cell culture, cryo-electron microscopy; X-ray crystallography; hydrogen-deuterium exchange mass spectrometry; biophysical measurements of assembly on membranes by confocal microscopy, flow cytometry and single-molecule fluorescence; and enzyme assays. The candidate should have a Ph.D. degree or due to complete doctoral studies within 6 months of applying. It is essential that the candidate has an enthusiasm for structural biology. Experience with electron microscopy, X-ray crystallography, mass spectrometry or large scale eukaryotic expression systems would be desirable, but a motivated candidate could learn any or all of these. The MRC Laboratory of Molecular Biology is one of the birthplaces of modern molecular biology and has amazing support for all aspects of structural biology. For full details, see the MRC link https://mrc.tal.net/vx/mobile-0/appcentre-ext/brand-3/candidate/so/pm/4/pl/… <https://mrc.tal.net/vx/mobile-0/appcentre-ext/brand-3/candidate/so/pm/4/pl/…> or contact Roger Williams: email rlw(a)mrc-lmb.cam.ac.uk <mailto:[email protected]> or phone: +44 1223 267094 Dr. Roger Williams, FMedSci rlw(a)mrc-lmb.cam.ac.uk <mailto:[email protected]> MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH UK Phone: +44 1223 267094

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Job opportunity at the NKI
by Anastassis Perrakis 26 Jan '16

26 Jan '16

We are looking for an enthusiastic co-worker who recently got a PhD in Structural Biology and has strong working experience in X-ray crystallography and a clear interest in cell biology mechanisms, aspiring to connect molecular chemistry and structure to the inner workings of a cell, using a wide portfolio of approaches. You will study with us the mechanisms that ensure correct chromosome segregation during cell division in a project with a two-fold scope. First, in collaboration with the group of Geert Kops (Hubrecht Institute) we want to determine new structures and understand the function of proteins that control spindle checkpoint signaling. Second, in collaboration with the EMBL Grenoble Unit and the Diamond Light Source in the iNEXT (www.inext-eu.org <http://www.inext-eu.org/>) project, we want to establish, benchmark and extend fragment-based screening, using as our major targets mitotic proteins we work on. The two projects are scientifically coherent and significant preliminary work is in place. You will be responsible for designing and executing all experiments as part of a small but lively team. The project will be supported by the NKI Protein Facility and state of the art instrumentation for expressing, purifying and crystallising proteins (including robotics), as well as a wealth of biophysical equipment, including surface plasmon resonance, microscale thermophoresis, isothermal titration calorimetry, fluorescence measurement, and light scattering. The NKI also offers a Robotics and Screening Centre, a Genomics core, Proteomics, Peptide synthesis, and Microscopy facilities. The group is hosted in the Department of Biochemistry, a diverse and lively environment with enthusiastic colleagues. The NKI is an integrated hospital and research centre for cancer, and is located within minutes from the centre of Amsterdam and it’s cultural amenities. The temporary employment will be for an initial period of 2 years. The gross salary per month will be ~3,300 Euro, according to the FWG-function group 55.6, or higher depending on previous experience. Foreigners are entitles to a 30% tax break, subject to a decision of the tax authorities. For further information please contact Anastassis Perrakis, a.perrakis(a)nki.nl <mailto:[email protected]>, or send directly your CV including the names of three referees, no later than 19 February. Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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Re: [phenixbb] [ccp4bb] Modify methionine to acetylated methionine in coot
by Anshul Bhardwaj 26 Jan '16

26 Jan '16

Thanks Paul for the quick response. Simple enough and works beautifully for modifying N-terminus methionine to AME in coot. Anshul Bhardwaj ________________________________________ From: Paul Emsley <pemsley(a)mrc-lmb.cam.ac.uk> Sent: Monday, January 25, 2016 7:39 PM To: Anshul Bhardwaj; COOT(a)jiscmail.ac.uk Subject: Re: [ccp4bb] Modify methionine to acetylated methionine in coot On 25/01/2016 23:33, Anshul Bhardwaj wrote: > Hello, Hello. > How to replace 'M' with 'AME' in coot itself? an option like mutate residue, etc. > I couldn't figure out right away so I worked my way around by simply copying AME from one of the pdb from RCSB database and replaced methionine in my model. Linked AME to residue# 2 in coot and refinement was straightforward after generating restraints for the modified model. So it worked for now but still curious as there has to be a way to replace 'M' with 'AME' in coot, isn't it (?). > Generally, for this sort of thing one would use: Extensions -> Modelling -> Replace Residue -> AME But this might not work in the case because the modification is on the main-chain not the side-chain. But it might do if the AME is at the N-terminus. This thread might shed some light on things: https://www.mail-archive.com/[email protected]/msg02536.html Paul. The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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Modify methionine to acetylated methionine in coot
by Anshul Bhardwaj 26 Jan '16

26 Jan '16

Hello, How to replace 'M' with 'AME' in coot itself? an option like mutate residue, etc. I couldn't figure out right away so I worked my way around by simply copying AME from one of the pdb from RCSB database and replaced methionine in my model. Linked AME to residue# 2 in coot and refinement was straightforward after generating restraints for the modified model. So it worked for now but still curious as there has to be a way to replace 'M' with 'AME' in coot, isn't it (?). Thanks, Anshul Bhardwaj P.S. Hope it's okay to cross-post on both ccp4bb and phenixbb to get an answer quickly. The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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Coot 3D for Geforce GTX 970 Graphics card on Windows 7 and Fedora
by Xiao Lei 25 Jan '16

25 Jan '16

Hi Phenixbb members, My lab has a desktop PC which has Windows 7 with Geforce GTX 970 Graphics card, is this card ok for the Coot 3D function with 3D monitor and Nvidia 3D kit? Do I need to do some settings before I can use the Coot 3D function? I'm also thinking installing Fedora 23 on the PC and use coot 3D, is there any settings in the Fedora environment before using coot 3D? Thanks ahead.

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Changing NCS groups
by Marie Elizabeth Fraser 25 Jan '16

25 Jan '16

Hello, I would like to edit the NCS information for a model with two chains. I've tried running find_ncs and editing the phil file, but I get an error when I try to use my edited file in the next cycle of refinement. I've tried using the utility to detect NCS groups, then edited in the little windows - also no success. How are other people defining NCS when they aren't content with the equivalences the program finds? Thank you for your insight, Marie

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Xtriage systematic results is not consistent with HKL2000
by Alex Lee 23 Jan '16

23 Jan '16

Dear All, I scaled a dataset of SG P2221 in HKL2000 and got systematic absence results as below, it seems clearly HKL2000 showed the data had systematic absence violations, but when I used the .sca file from HKL2000 as input in Xtriage, the result did not show any systematic violations. Which result should I rely on? HKL200 Results: Summary of reflections intensities and R-factors by shells R linear = SUM ( ABS(I - <I>)) / SUM (I) R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2) Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) ) In all sums single measurements are excluded Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac Rmeas Rpim CC1/2 CC* 50.00 5.60 2819.0 103.7 44.8 0.607 0.033 0.040 0.037 0.017 0.998 0.999 5.60 4.45 1801.5 63.8 28.1 0.914 0.043 0.050 0.048 0.022 0.997 0.999 4.45 3.88 1435.3 52.6 25.5 0.980 0.048 0.051 0.054 0.024 0.997 0.999 3.88 3.53 738.7 31.8 20.5 1.117 0.068 0.067 0.075 0.032 0.996 0.999 3.53 3.28 489.7 26.5 20.1 1.134 0.092 0.080 0.102 0.043 0.996 0.999 3.28 3.08 236.3 19.8 17.4 0.975 0.147 0.108 0.162 0.069 0.993 0.998 3.08 2.93 93.4 16.4 16.0 0.850 0.296 0.277 0.327 0.138 0.947 0.986 2.93 2.80 62.9 16.3 16.0 0.737 0.422 0.384 0.467 0.197 0.921 0.979 2.80 2.69 42.6 16.7 16.5 0.677 0.622 0.515 0.688 0.291 0.879 0.967 2.69 2.60 29.3 20.0 19.9 0.680 0.924 0.842 0.000 0.440 0.659 0.891 All reflections 798.1 37.4 22.6 0.873 0.064 0.050 0.068 0.031 Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 3 -0.4 1.3 -0.3 0 0 5 10.4 3.0 3.5 0 0 7 11.4 3.9 2.9 0 0 9 8.7 4.3 2.0 0 0 11 18.6 6.4 2.9 0 0 13 182.9 17.1 10.7 0 0 15 3.0 7.8 0.4 0 0 17 11.9 9.2 1.3 0 0 19 30.0 14.3 2.1 0 0 21 7.4 11.1 0.7 0 0 23 54.2 15.6 3.5 0 0 25 43.1 16.1 2.7 0 0 27 12.5 18.9 0.7 0 0 29 -16.6 20.9 -0.8 0 0 31 31.0 25.4 1.2 0 0 33 3.4 29.2 0.1 0 0 35 -24.2 32.0 -0.8 0 0 37 50.9 42.5 1.2 0 0 39 -53.3 66.4 -0.8 0 0 41 65.8 50.6 1.3 0 0 43 -24.3 46.8 -0.5 0 0 45 -6.1 48.3 -0.1 0 0 47 -14.8 45.8 -0.3 0 0 49 1.1 53.5 0.0 0 0 51 -7.9 64.2 -0.1 Phenix Xtriage Results: ----------Space group identification---------- Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of systematic absence violations are listed under the '+++' column. The number of non-absence violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ------------------------------------------------------------------------------------- | space group | # absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ------------------------------------------------------------------------------------- | P 2 2 2 | 0 | 0.00 | 0.00 | 0 | 4 | 0.000e+00 | | P 2 2 21 | 0 | 0.00 | 0.00 | 0 | 4 | 0.000e+00 | | P 2 21 2 | 5 | 3.07 | 16.77 | 5 | 4 | 1.038e+01 | | P 2 21 21 | 5 | 3.07 | 16.77 | 5 | 4 | 1.038e+01 | | P 21 2 2 | 5 | 1.89 | 15.21 | 5 | 4 | 1.250e+01 | | P 21 2 21 | 5 | 1.89 | 15.21 | 5 | 4 | 1.250e+01 | | P 21 21 2 | 10 | 2.48 | 15.99 | 10 | 4 | 2.288e+01 | | P 21 21 21 | 10 | 2.48 | 15.99 | 10 | 4 | 2.288e+01 | ------------------------------------------------------------------------------------- ----------List of individual systematic absences---------- Note: this analysis uses the original input data rather than the filtered data used for twinning detection; therefore, the results shown here may include more reflections than shown above. P 2 2 2: no systematic absences possible P 2 2 21 (input space group): no absences found P 21 2 2 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 2 21 2 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 P 21 21 2 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 2 21 21 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 P 21 2 21 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 21 21 21 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 Thanks ahead

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Change of PHIL definitions in phenix.find_alt_orig_sym_mate
by R.D. Oeffner 22 Jan '16

22 Jan '16

I have changed the PHIL definitions in this program from AltOrigSymMates.moving_pdb to AltOrigSymMates.moving.pdb and from AltOrigSymMates.fixed_pdb to AltOrigSymMates.fixed.pdb. I'm not sure if it is being used elsewhere but let me know if you encounter an error due to this. Regards, Rob

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anomalous completeness from Phenix Xtriage result
by Alex Lee 22 Jan '16

22 Jan '16

Dear All, After check my data with Phenix Xtriage, I got a warning of "the anomalous completeness is 42.34%". I do not know if I need to pay attention to this? I did not do experimental phasing and I did not add heavy metal to my crystal nor there is selenium on my protein. I even don't know why I still get the anomalous signal. But from the detailed summary below I guess in my case it's not a problem? ----------Summary---------- File name: P2_rejoutput.sca Data labels: I(+),SIGI(+),I(-),SIGI(-) Space group: P 1 2 1 Unit cell: 72.255, 46.617, 134.086, 90, 90.052, 90 Data type: xray.intensity Resolution: 49.1682 - 2.5855 Anomalous: True Number of reflections (non-anomalous): 27184 Completeness (non-anomalous): 95.42% Number of reflections (all): 38285 Completeness (all): 69.98% Anomalous completeness: 42.34% Completeness (non-anomalous) is the completeness of the data after merging Friedel pairs. Completeness (all) is the completeness of the data before merging Friedel pairs. Completeness (anomalous) is the completeness of the anomalous data. The anomalous completeness is calcluated by dividing the number of measured acentric, Bijvoet mates by the total possible number of acentric indices. Completeness (non-anomalous) should be used to determine if there is sufficient data for non-anomalous purposes (refinement, model-building). A value greater than 90% is generally desired, while a value less than 75% is considered poor. Values in between will provide less than optimal results. Completeness (anomalous) should be used to determine if there is sufficient data for anomalous purposes (phasing, finding anomalous atoms, refinement of anomalous occupancies or scattering factors). A value greater than 80% is generally desired, while a value less than 50% is considered poor. Values in between will provide less than optimal results. Thanks.

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Specify a chain in Phenix Autobuild
by Xiao Lei 21 Jan '16

21 Jan '16

Hi Phenixbb members, I am using Phenix autobuild for a protein-DNA complex. There are three chains for protein (F, H, I) and two chains for DNA (A and B). I know Autobuild can only build one chain at a time and I'm only going to build chain F. In the autobuild GUI, I can find an option of Chain type "Auto", "protein" , "DNA" and "RNA". Is there a place in the GUI which I can specify only building protein chain "F"? Thanks ahead.

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ligand modification / combination in REEL
by andre.stiel 20 Jan '16

20 Jan '16

Hi, I have a phosphatidyl inositol ligand without an existing CIF file only smiles. When I construct the ligand from the smiles ELBOW regards the sugar as just an aromatic ring. So I see three possibilities how to end up with a proper constraints file for my ligand (that is: tails like in the smiles but with a proper sugar (chair) conformation on top): 1. Can I edit the aromatic ring in REEL in a way to push it into the desired boat/chair conformation? I did not find a command to that end although he can clearly „see“ this conformation as I know from another ligand. 2. Can I chop the sugar part from the .CIF of another ligand and somehow fuse it to my tails? 3. There is a sugar editor in REEL (which however crashes at the moment for me (Version 1-10-2155)) can I use this to construct the desired sugar and somehow fuse it to the rest… basically like option 2? I have not found a very extensive documentation on how to play such tricks with REEL. Or would I have to rebuild a complete ligand with this SCALES? Other suggestion how to get my ligand are also welcome. Thanks André Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

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N-acetylgalactosamine lacking amide planarity restraint
by Tristan Croll 20 Jan '16

20 Jan '16

Hi, I'm refining a structure that includes an O-linked N-acetylgalactosamine (NGA) residue, and from the way it's behaving the N-acetyl amide clearly has no restraints on its planarity. It's currently twisted almost 45 degrees from planar despite having no close contacts. Cheers, Tristan

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how not to refine residue X?
by Murpholino Peligro 19 Jan '16

19 Jan '16

Hi. How to tell phenix.refine to leave residue X during refinement? I already tried in the .eff >>> strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous sites { individual = not (chain A and resid 97) <<< But resid 97 is being moved to another position. I am using phenix.refine_1.10.1-2155 Thanks

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phenix.sort_heteroatoms produced duplicated residue number
by luzuok 13 Jan '16

13 Jan '16

Dear phenixbb, When I use phenix.sort_hetero_atoms to resort my pdb, there are duplicated residue number of water and aa in the output pdb. Is this a bug? As there are many number gaps water, how can I fix it? Best wishes! Lu -- 卢作焜南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

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pdbtools model_statistics: average B-factors
by wtempel 12 Jan '16

12 Jan '16

Hello, are the mean B-factors in the "ADP statistics" table occupancy-weighted, or perhaps weighted in any other way? If so, please could you provide the formula. Thank you. Wolfram Tempel

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phenix.refine with reference model
by Falk, Sebastian 08 Jan '16

08 Jan '16

Hi! I am currently building a 3.3 A structure of a large protein. I do have a reference model at much better resolution that has 58% sequence identity and 77% similarity. The structures are quite similar, there are only a few regions with insertions. However, phenix.refine does ‘accept’ the reference model and thus creates no torsion restraints. I also tried to run ProSmart in CCP4 but there the cut-off for the reference model is 75% sequence identity. I could not find any threshold for phenix.refine though. I am happy for any suggestion or tip how to include the reference model even though the sequence identity is not as high. Thank a lot. Sebastian Sebastian Falk Max-Planck-Institute for Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany sfalk(a)biochem.mpg.de

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Generate sequence files of homodimer protein or double strand DNA for phaser MR
by Alex Lee 08 Jan '16

08 Jan '16

Dear Phenixbb members, I am using Phaser MR for solving a homodimer DNA binding protein with dsDNA complex structure. I'd like to use sequence file rather then molecular weight in the component definition of ASU. As there are solved homodimer protein structures (amino acid identity 100%) on PDB, I can download seq file (fasta form) from PDB webpage, but the seq file is only for one protein chain. I also tried online tools like "make sequence from PDB file" (http://swift.cmbi.ru.nl/servers/html/soupir.html), when I put the protein dimer bound to dsDNA pdb into the online tool, the outtput pir sequence file only shows a single protein chain and dna which dose not seems like two strands, rather then just put two 23base dna together for a 46 base length single strand DNA. I am asking is there a way to generate sequence file for a homodimer and dsDNA? or I have to generate sequence file for each chain separately (there will be four sequence files in this case, two protein chains and two dna chains)? Thanks. Alex Alex

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coot generate symmetry mates like pymol
by Xiao Lei 08 Jan '16

08 Jan '16

Hi Phenixbb members, 1. Is there a function in coot which can generate symmetry mates like pymol (action--> generate symmetry mates)? I know in coot there is a "Draw---> Cell&Symmetry" function, but it seems the display results could not display my crystal packing like pymol. 2. In pymol, is there a button which just display structure in one unit cell? Thanks. Xiao

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unwanted N/Q/H flipping in PHENIX.REFINE
by Bernhard Loll 05 Jan '16

05 Jan '16

Dear all, I am currently refining a 1.9 A structure with PHENIX 1.10.1-2155. The problem I am facing is the following: Running the Molprobity server, it suggests me to correct a couple of N/Q/H flips. I perform the flips re-run PHENIX.REFINE with “Automatically correct N/Q/H errors” not ticked. The log file confirms the selection with nqh_flips = False. Nevertheless PHENIX.REFINE again flips these residues and the output PDB file has all previously flipped residues “re-flipped” in comparison to the input PDB file. I am very confident that the automatically flips performed by PHENIX.REFINE (REDEUCE) are wrong, since I have two metal binding sites. Why PHENIX.REFINE rotates side chains by 180 degree even though nqh_flips were set to false? Any help is appreciated. Cheers, Bernhard Dr. Bernhard Loll Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fuer Chemie und Biochemie AG Strukturbiochemie Takustr. 6 D-14195 Berlin Germany Phone: +49 (0) 30 838-57348 Fax: +49 (0) 30 838-454936 Email: loll(a)chemie.fu-berlin.de Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/

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Project info lost after a disk crash
by hli 04 Jan '16

04 Jan '16

Hi, The hard drive of our major Linux computer crashed recently. After installing a new disk and recovering all the data in the damaged disk I lost all the project information in PHENIX GUI home page. I noticed that under .phenix directory there are files like project_db.pkl, but do not know how to retrieve the old project info into the GUI. Thanks in advance for your help. Huiying Dept. MB&B UC Irvine

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Re: [phenixbb] Modifications for Ca-binding site
by Nigel Moriarty 30 Dec '15

30 Dec '15

Jacob Once again Boaz is leading you in the correct direction. You did send me a *.metals.edits file. You just need to change the ideal distances in this file. On another point, I ran a refinement with your inputs and the values don't seem a long way off. However, I'd wait for Pavel to take a look because the density around the Calcium ion itself seems unusual. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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 On Wed, Dec 30, 2015 at 6:27 AM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi Jacob, > > My guess is that answer (or hint) is here (taken from this link : > https://www.phenix-online.org/documentation/faqs/refine.html#targets-and-re…): > > > *I have ions very close to water molecules/protein atoms, and > phenix.refine keeps tring to move them apart. How can I prevent this?* > > Use phenix.ready_set or *phenix.metal_coordination* to generate custom > bond (and optionally, bond angle) restraints, which will be output to a > parameter file ending in ".edits". If you are using the PHENIX GUI, there > is a toolbar button for ReadySet in the phenix.refine interface, which will > automatically load the output files for use in phenix.refine. > > I have not used it myself but I assume that the sigmas for the restraints > would be in the *.edits files that you'll generate. > > Hope this helps. > > Boaz > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > ------------------------------ > *From:* Keller, Jacob [kellerj(a)janelia.hhmi.org] > *Sent:* Wednesday, December 30, 2015 4:09 PM > *To:* Nigel Moriarty > *Cc:* בעז שאנן; phenixbb(a)phenix-online.org > *Subject:* RE: [phenixbb] Modifications for Ca-binding site > > How does one change the ideal bond length/sigma in Phenix? > > > > JPK > > > > *From:* Nigel Moriarty [mailto:[email protected]] > *Sent:* Tuesday, December 29, 2015 10:12 AM > *To:* Keller, Jacob > *Cc:* Boaz Shaanan; phenixbb(a)phenix-online.org > *Subject:* Re: [phenixbb] Modifications for Ca-binding site > > > > Jacob > > > > Boaz has some sage advice. I recommend not excluding the Ca-O coordination > but changing the ideal to better reflect the distances in your files. > > > > PS I'd also like the PDB files, directly, so as not to put noise on the > list. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, 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 > > > > On Tue, Dec 29, 2015 at 5:49 AM, Keller, Jacob <kellerj(a)janelia.hhmi.org> > wrote: > > Well, I think it's more of a data-vs-geometry battle, with the geometry > dragging in the side chains towards the calciums, and the data pulling them > out. When I real-space refine them in Coot, some of the Ca-O distances are > pretty different from the "ideal" values. Maybe I could just exclude them > from xyz refinement in Phenix after making sure they're correct in Coot? > I'll give that a shot. > > Kol tuv, > > Jacob > > > > > > -----Original Message----- > From: Boaz Shaanan [mailto:[email protected]] > Sent: Tuesday, December 29, 2015 7:52 AM > To: Keller, Jacob; phenixbb(a)phenix-online.org > Subject: RE: Modifications for Ca-binding site > > Hi Jacob, > > Sucking-up neighboring residues into the Calcium (or other heavier atoms) > density is a known issue. Turning-off the Ca-O or other distance restraints > around the Calcium is the last thing you want to do, in my experience. > You'd better check those distance restraints and verify that they're > compatible with the distances in other (preferably high resolution, of > course) structures with calcium binding sites similar to yours and then > make sure they're given the appropriate weight during refinement. That's my > view but Pavel will give you more advices I'm sure. > > Cheers, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org [ > phenixbb-bounces(a)phenix-online.org] on behalf of Keller, Jacob [ > kellerj(a)janelia.hhmi.org] > Sent: Tuesday, December 29, 2015 4:44 AM > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Modifications for Ca-binding site > > I am getting a lot of problems with my calcium binding sites--there is > clear density for the calciums and the protein side chains, but Phenix > keeps sucking the side chains out of their density towards the calciums and > also the calciums show some positive difference density, perhaps due to > too-high b-factors (or potentially partial occupancy by Na?). I think what > might work best is to turn off the Ca-O bond length restraints somehow, but > don't see where/how to do that. I tried releasing them from geometrical > restraints, but that made things worse, since things went haywire in the > sidechains themselves. > > Is it possible to make Phenix ignore the Ca-O bond distance restraints? > > JPK > > ******************************************* > Jacob Pearson Keller, PhD > Looger Lab/HHMI Janelia Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > email: kellerj(a)janelia.hhmi.org > ******************************************* > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

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Modifications for Ca-binding site
by Keller, Jacob 30 Dec '15

30 Dec '15

I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints, but that made things worse, since things went haywire in the sidechains themselves. Is it possible to make Phenix ignore the Ca-O bond distance restraints? JPK ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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RSRZ in Phenix?
by Keller, Jacob 30 Dec '15

30 Dec '15

Dear Crystallographers, Is there any place in Phenix where RSRZ or a similar measure is shown? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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Coot add DNA base or mutate DNA base
by Xiao Lei 25 Dec '15

25 Dec '15

Hi All, I'm using coot to build DNA, when I click "add residue" to one end of DNA, coot automatically add an "A" base to it, but I'd like to add "G" base, is it a way to mutate the A base to G base, I know coot can mutate amino acid residue, is is a way to mutate DNA residue in coot GUI? Thanks ahead. Xiao

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Trouble refining following molecular replacement
by Tyler Liban 22 Dec '15

22 Dec '15

Hello all, We are currently working with a dataset for a trimeric protein complex at 3A that is giving us some issues. The space group seems to be P21 ( 59.5, 61.6, 99.6 , 90, 98, 90) and the Mathews coefficient (2.6) suggests 2 copies of this 35kDa complex in the ASU. We are using a homolog as the search model that is 80% identical, and Phaser is able to find 2 molecules in P21 when searching in the same point group and gives good TFZ scores (TFZ = 9 or 10). However, these solutions do not refine well following Phaser (Rfree ~.50), and after removing parts of the model that look incorrect the Rfree still stays between .46 and .50. We ran the data through Xtraige and saw no signs of twinning based on the L-test, and the Patterson map has one small off-origin peak that is only 5%, indicating that there is no significant pseudotranslation. We have also tried finding MR solutions in P1, but haven’t had much luck. Any ideas on where to go from here would be greatly appreciated. Tyler

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command line for reflection file editor
by Zheng Zhou 22 Dec '15

22 Dec '15

Dear phenix experts, How do I combine Rfree from one dataset with the new dataset under command line? I can do this using reflect file editor GUI easily. But I tried to look up the documentation for phenix.reflection_file_converter and could not find a solution. I am trying to write a script to handle several datasets scaled from HKL2000. I could do this easily in ccp4, but looks like Ctruncate's French&Wilson made the completeness worse than scale.log. Thanks for your help in advance. Best, Zheng

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mmCIF file must contain at least one data block
by Ursula Schulze-Gahmen 18 Dec '15

18 Dec '15

I am getting this thie error message mmCIF file must contain at least one data block when trying to run readyset or phenixrefine I cannot find anything wrong wqith my input files. What is the problem? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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remove old phenix version but keep the processed data
by Xiao Lei 17 Dec '15

17 Dec '15

Hi Phenixbb member, As I updated Phenix version on my Macbook pro (OS X 10.10), I found the newer version phenix did not automatically replace the old versions. Is there a way to remove the old version Phenix safely and only keep the newer version, but at the same time keep the processed data (data from phenix refine and xtriage)? Thanks ahead. Xiao

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ML with Twinning?
by Keller, Jacob 16 Dec '15

16 Dec '15

Is Phenix able yet to use the ML target function with twinned data? Is it in the works? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Ezequiel Noguera 16 Dec '15

16 Dec '15

Thank you very much, Pavel. I don't save H's when I modify the model in coot (the input PDB file that I sent you was the output from coot). I did the refinement again, now in version 2247, without NCS. I got the same results, higher R factors and RMS deviations for the newer version. I got better results when I used "update waters" (both in Rfactors and RMS). Below, I list the statistics for refinement without updating waters. Significant differences remain. Could it be any difference in settings of default parameters between versions? version: dev-2247 Start: r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles = 1.321 Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030 angles = 0.593 version: 1.9-1692 Start: r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles = 1.409 Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321

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Re: [phenixbb] -differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Pavel Afonine 13 Dec '15

13 Dec '15

Hi Ezequiel, just to make it clear: torsion-angle NCS, Optimize X-ray/stereo weight are *not* the default settings, therefore you did customize the refinement parameters. At this resolution (1.3A) you do not need to use NCS restraints. Also, you say you used "Automatically add H's" however the PDB file you sent me does not contain any H atoms. Furthermore, the PDB file header says H are present: REMARK MODEL CONTENT. REMARK ELEMENT ATOM RECORD COUNT OCCUPANCY SUM REMARK C 1275 1047.00 *REMARK H 2029 1649.00 * REMARK O 559 488.50 REMARK N 315 263.00 REMARK S 6 6.00 REMARK Cu 4 2.89 REMARK TOTAL 4188 3456.39 So overall this make an impression that something has gone wrong. Way forward: 1) Take the file you sent me; 2) Add H atoms: phenix.reduce model_no_h.pdb > model_with_h.pdb 3) Use new file with H atoms added to run refinement. The only setting different from defaults should be "Optimize X-ray/stereo weight". Perhaps you can also enable automated water update. I just did all this myself and got nicely refined model with Final: r_work = 0.1624 r_free = 0.1939 bonds = 0.010 angles = 1.030 Corresponding PDB and MTZ are sent in a separate email that goes to you only (off mailing list). Pavel On 12/6/15 07:59, Ezequiel Noguera wrote: > Hi Pavel, thank you very much for your help. I attach the data. I > didn´t customize parameters. The refinement stategy of the last job > was: XYZ coords, Real-space, Individual B-factors, torsion-angle NCS, > Optimize X-ray/stereo wght and X-ray/ADP wght, Automatically add H's > and correct N/Q/H errors. > > > Hi Ezequiel, > > deviations are not unexpected in general but not that large as you > report, so I wonder what's going on.. Could you please send me input > data and model files, as well as any ligand files you used. If you > customized some parameters, telling what were those would be helpful too. > > Please send all files off-list to my email directly. > > Thanks, > Pavel > > >> Hello, I'm working in a refinement that I started some time ago. I >> noted that repeating the same refinement task using a newer version >> of phenix, the refinement statistics Before and After refinement are >> different from values of the old version (I used "restore job" from >> the Job history to repeat the same task in the two versions installed >> in the same PC). Any explanation? I'm worried about the rms >> deviation. Thanks in advance. >> >> new version: >> R-work: start=0.1697, final=0.1761 >> R-free: start=0.2011, final=0.2053 >> Bonds: start=0.046, final=0.029 >> Angles: start=1.321, final= 0.631 >> >> old version: >> R-work: start=0.1651, final=0.1657 >> R-free: start=0.2018, final=0.2009 >> Bonds: start=0.013, final=0.013 >> Angles: start=1.409, final= 1.411

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autosolve density modification question
by Scott Horowitz 10 Dec '15

10 Dec '15

Hi, a quick question: if when running autosolve on SAD data, if I set the parameter build = false, will that disable all model building, including any model building that would be a part of the density modification process? I'm especially curious about the case if build = false, but mask_type = histograms. I am currently assuming that the histogram matching does not use model building as part of it, and would like to know if this interpretation is correct. Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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