- phenixbb - phenix-online.org

Trouble with occupancy refinement
by Chris Fage 09 Feb '16

09 Feb '16

Hello, I've built several glucose molecules from my cryosolution into regions of weaker electron density. Attempting to refine the occupancies of the corresponding atoms, I set the value of each to 0.25 in the pdb file. However, after running phenix.refine, most of the atoms still have occupancies of 1.00: 14 atoms with occ = 0.00 5 atoms with 0.00 < occ < 1.00 74 atoms with occ = 1.00 Is this unusual? Thank you! Best, Chris

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Re: [phenixbb] sequence independent model building possible?
by Kay Diederichs 09 Feb '16

09 Feb '16

To check if you crystallized a contaminant, use https://strube.cbrc.kaust.edu.sa/contaminer/ HTH, Kay > >On 02/05/2016 01:01 AM, Kaushik Hatti wrote: >> 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 >> >> -- > -- Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.

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Dual conformation on symmetry axis
by Jan Abendroth 06 Feb '16

06 Feb '16

Hi all, I am running into the following problem during the refinement of a rather small structure at 2.15Å resolution: An Arg side chain is located very close to a crystallographic 2-fold. There is good evidence that the side chain has two conformations. However, because of the 2-fold, conformer A overlaps with its symmetry mate A*, as does conformer B. Phenix wants to avoid this 'clash' and moves A and A* out of the density, same for B and B*. Is there a way to avoid this without reducing the symmetry? In the real crystal, of course the two side chains are agnostic as to if they are called A or B and will avoid one another ... Thanks! Jan -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

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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 25 Jan '16

25 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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