February 2016 - phenixbb - phenix-online.org

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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