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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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