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Announcing the 2015/2016 EMDataBank Model Challenge
by Cathy Lawson 14 Oct '15

14 Oct '15

Dear PhenixBB List Members, EMDataBank is pleased to announce the 2015/2016 Model Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Benchmark targets of varying size and complexity have been selected from recently deposited 3DEM structures based on current state-of-the-art detectors and processing methods, in the resolution range 2.2-4.5 Å. Challengers are sought to create and validate models from challenge target maps in four different categories (1. optimize current cryoEM model, 2. fit known related cryoEM, crystallographic, or comparative models, 3. ab initio model building, 4. any other method of map interpretation), and upload their results with associated details. Assessors are sought to participate in evaluating submitted models. Registration is now open for all interested participants. Challengers may submit their models between November and April. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in late 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MODEL CHALLENGE" in the menu bar. This is the second of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. The first challenge is focused on creating reconstructions from raw 2D image data and is currently in progress (click on "MAP CHALLENGE" in the menu bar). Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Model Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

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Question regarding uploading 2Fo-Fc map into KiNG
by Natalia Ketaren 07 Oct '15

07 Oct '15

Hello All, I have a question regarding the KiNG program: I used MolProbity to assess the quality of my model which revealed some poorly fitted residues in my structure. I want to correct these residues using KiNG but am having problems uploading the electron density map. Does the program not accept .mtz maps generated by coot? Do I have to convert the map into another file format? If so, would you be able to suggest a program for me with which to do this? Any help would be greatly appreciated! Kind regards, Natalia _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

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Phenix bug fix version 1.10.1 released
by Paul Adams 07 Oct '15

07 Oct '15

A bug fix version of Phenix is now available (build 1.10.1-2155). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ This addresses the following issues: - Incorrect location used for heavy atom files when running AutoBuild in certain circumstances - Errors when adding hydrogens to waters in ReadySet - Errors when using GUI helper applications that handle sequences (e.g. Blast search) Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Answer regarding uploading 2Fo-Fc map into KiNG
by Christopher Williams 07 Oct '15

07 Oct '15

Hi Natalia, Thanks for your use of MolProbity and your interest in improving models. It means a lot to us. As you have noted, MolProbity indeed does not accept .mtz files. It accepts 3 file formats for electron density maps: OMAP, CCP4, and XPLOR. Fortunately, Phenix can generate maps for you. In the Phenix GUI, there are two relevant options under the "Maps" tab. The first one, "Calculate maps", can turn structure factors into .mtz or .ccp4 . The second one, "FFT map coefficients", can use a .mtz to generate a .ccp4 or a .xplor, and is probably the option you are looking for. Someone more familiar with the Phenix commandline may be able to tell you how to generate maps from the commandline in a more scriptable way. Hopefully this helps, -Christopher Williams ---Richardson Lab, Duke University

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on cif file
by Smith Lee 06 Oct '15

06 Oct '15

Dear All, For the phenix refine of a protein-ligand complex, is the ligand cif file a necessity? If we do not add the cif file, what will occur? Best regards. Smith

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Special position ambiguity
by R Sarath 06 Oct '15

06 Oct '15

Hi, I have to place two carbon atoms (C3 and C6 - in para positions) of a cyclohexane ring from a ligand in special positions (I4122 space-group), with C6' from the symmetry generated molecule overlapping on C3 of the ligand. Can someone please suggest me a way to do so. I tried changing the occupancies of C3 and C6 to 0.5. After refinement, I observe that they don't overlap but instead spoil the fitting of neighbouring atoms of the ligand. Thanks in advance, Regards,Sarath

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on ligand restraint
by Smith Lee 05 Oct '15

05 Oct '15

Dear All, Does phenix.refine can process some ligands without the process by eLBOW, for example ATP, ADP,etc? Smith

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Selection of Torsion NCS restraint groups
by Victor Xiao 04 Oct '15

04 Oct '15

Dear all, I have a protein-DNA structure that has six molecules in ASU. All six molecules share the same sequence and very similar structure. However, only three of them bind to DNA and conformations are slightly different from the other three. By default, PHENIX will consider six molecules into the same NCS group. Now I am trying to set up two NCS group, e.g. chain A,B,C are in one group (no-DNA), chain D, E, F are in another group (DNA-bound). So I did the following steps: 1. I used PHENIX GUI and go to 'Utilities' -> 'Detect NCS Groups'. 2. Put chain A, B, C in 'Torsion NCS restraint group 1'. 3. 'Add group' and put chain D, E, F in 'Torsion NCS restraint group 2'. 4. Click 'Update and exit'. However, after that, when I re-open 'Utilities' -> 'Detect NCS Groups', I found all six chains A-F are in group 1, and all six chains A-F in group 2. Did I do something incorrectly? Or any other suggestion for my purpose? Thank you! Best, Xiao

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Phenix eLBOW output cif missing Chi angle information
by Xiao Lei 02 Oct '15

02 Oct '15

Hi Phenix BB members, I tried to generate restraints of 3-METHYL-BETA-D-ASPARTIC ACID (PDB 3 letter code ACB, http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=ACB). I am using this as a template for D-iso-aspartic acid in my model because I can not find a 3 letter code for the exact D-iso-aspartic acid (I know for L-iso-aspartic acid the code is IAS but no code for D-iso-aspartic acid) I can search in Phenix eLBOW (Mac Phenix Version 1.10pre) with code ACB and I can find the code and right compound, I tried to generate restraints of ACB using eLBOW and I got a cif and pdb output of the compound. However when I import the compound into coot, delete the methyl group to make the compound a D-isoAsp, and click "edit chi angles", I receive an error: This residue does not have assigned torsion/chi angles". I do not know what I should do to fix the problem. I thought eLBOW would automatically generate Chi angles but actually it did not in my case. I appreciate if you have any input on this. [image: Inline image 1]

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Non crystallographic symmetry
by Reza Khayat 02 Oct '15

02 Oct '15

Hi, I need to use icosahedral symmetry to refine a virus crystal structure. Does phenix support 60 NCS matrices? If not, how should I go about recompiling the program so that I can have 60 NCS matrices? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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