- phenixbb - phenix-online.org

phenix install error on linux
by Min Zheng 11 Feb '16

11 Feb '16

Dear All, I am installing phenix, and get the following error: ========================================================================== Phenix Installation version: 1.10.1-2155 machine type: intel-linux-2.6-x86_64 OS version: 3.11.10-29-default destination: /home/m/m_zhen01/phenix-1.10.1-2155 # of processors: 20 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/nfsexp/homes/m_zhen01/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 "/nfsexp/homes/m_zhen01/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 "/nfsexp/homes/m_zhen01/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 "/nfsexp/homes/m_zhen01/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/m/m_zhen01/phenix-1.10.1-2155/base/bin/python /home/m/m_zhen01/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/m/m_zhen01/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 1 m_zhen01@LIBRA:~/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5> /home/m/m_zhen01/phenix-1.10.1-2155/base/bin/python Traceback (most recent call last): File "/usr/lib64/python2.7/site.py", line 564, in <module> main() File "/usr/lib64/python2.7/site.py", line 546, in main known_paths = addusersitepackages(known_paths) File "/usr/lib64/python2.7/site.py", line 276, in addusersitepackages user_site = getusersitepackages(kind) File "/usr/lib64/python2.7/site.py", line 244, in getusersitepackages user_base = getuserbase() # this will also set USER_BASE File "/usr/lib64/python2.7/site.py", line 230, in getuserbase from sysconfig import get_config_var File "/usr/lib64/python2.7/sysconfig.py", line 10, in <module> 'stdlib': '{base}/'+sys.lib+'/python{py_version_short}', AttributeError: 'module' object has no attribute 'lib' Thanks in advance, Min

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Refinement differences?
by Mark A Saper 11 Feb '16

11 Feb '16

Hi, I used Phenix, build 2037 to refine a a new structure. I reran the refinement (with the identical parameters) in build 2155 (v1.10.1) and obtained different statistics and slightly worse geometry. Any idea why? In 2037: start final --------------------------------------- R-work: 0.2488 0.2244 R-free: 0.3003 0.2851 RMS(angles): 1.67 0.80 RMS(bonds): 0.020 0.004 Ramachandran outliers: 1.2% (Goal: < 0.2%) Ramachandran favored: 94.5% (Goal: > 98%) Rotamer outliers: 8.7% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 3.14 Overall score: 2.19 2155 start final --------------------------------------- R-work: 0.2488 0.2331 R-free: 0.3003 0.2856 RMS(angles): 1.77 0.72 RMS(bonds): 0.020 0.004 Ramachandran outliers: 1.4% (Goal: < 0.2%) Ramachandran favored: 93.4% (Goal: > 98%) Rotamer outliers: 9.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 4.10 Overall score: 2.36 _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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differentiate Glu/Gln and Asp/Asn from Electron Density?
by Kaushik Hatti 11 Feb '16

11 Feb '16

Hello, In continuation to my earlier thread (subject: sequence independent model building possible?), I have built model into density without knowledge of sequence for a data diffracted to 1.9A resolution. Current R/Rfree is 15/19, phaser error=16.88 degrees with no Ramachandran outliers. Is there a way we can differentiate between Glu/Gln, Asp/Asn and sometimes Thr/Val directly from density? I have considered the local environment (hydrophobic/hydrophilic/polarity pockets, possible hydrogen bonds/other interactions, buried/exposed, etc...) in choosing one over the other confusing pairs of amino acids. However, I am not absolutely certain in many places. A BLAST of this sequence against all non-redundant protein sequence database yield highest hit of 80% sequence identity. Hence, we are still not sure of sequence of the contaminant protein which got crystallised and want to decipher sequence directly from the structure. Thanks for any pointers/suggestions, Regards, Kaushik -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

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Creating cyclic peptide coordinates and restraints
by A User 11 Feb '16

11 Feb '16

Hi Everyone, I am working on a 1.9A enzyme inhibitor complex. The inhibitor is a macrocyclic peptide with a non-proteinogenic amino acid that is modified at the n-terminus with a chloroacetyl-group that cyclizes via the sulfhydryl group of the next cysteine. The total lenght of the peptide is 9 amino acids. What is the most straight forward way to generate the coordinates of such macrocyclic peptide and what are the best settings in eLBOW to generate the restraints for it? Thanks for your time guys! Ben

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"Use starting structure as reference" for homo-multimers
by Tristan Croll 10 Feb '16

10 Feb '16

Hi, I've noticed that when I choose the option to use the starting structure as a reference model and my structure is a homo-multimeric protein, Phenix uses only the first chain as the reference for all chains during refinement. Personally I'd much prefer it if instead it ran a true 1:1 reference throughout the structure, since I tend to use this for final very fine-scale refinement of structures where I've already identified and modelled differences between NCS copies. Others' mileage may vary, of course. Best regards, Tristan

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Re: [phenixbb] Refinement differences?
by Mark A Saper 10 Feb '16

10 Feb '16

Hi Eckhard, Thanks for commenting on this. Unfortunately the data is not good, so I am cutting it off at 2.6 Å resolution. I probably won’t completely refine this structure. It does have 2 molecules in different conformations in the asymmetric unit so I could try NCS. -Mark On Feb 10, 2016, at 10:51 AM, phenixbb-request(a)phenix-online.org wrote: > From: Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> > Subject: Re: [phenixbb] Refinement differences? > Date: February 10, 2016 at 10:51:08 AM EST > To: phenixbb(a)phenix-online.org > > > Dear Mark, > there were chances to the geometry restraints which most likely would affect your refinement. > Do you have NCS in your refinement? This has been overhauled completely, and is currently not very verbose. > Generally I would not be very concerned about the exact values, given changes in the program. And it looks to me that you are not yet at the final point of refinement anyway. > What is your resolution? > All the best, > Eckhard

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Computational Crystallography Newsletter, Volume 7, Number 1
by Nigel Moriarty 09 Feb '16

09 Feb '16

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2016 <http://www.phenix-online.org/newsletter/CCN_2016_01.pdf> Short Communications - Characterization of base pair geometry <http://www.phenix-online.org/newsletter/CCN_2016_01.pdf#page=5> - Visual representations of internal coordinate restraints: Advantages and limitations <http://www.phenix-online.org/newsletter/CCN_2016_01.pdf#page=9> Fitting tips #11 – Can a helical DNA basepair be Hoogsteen? <http://www.phenix-online.org/newsletter/CCN_2016_01.pdf#page=3> 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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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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