<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks Paul, That is a lot of improvements!<br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Arial; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; 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"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Arial; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">With my best regards,</span></span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Tim</span></span></div><div style="font-family: Arial; "><br class="khtml-block-placeholder"></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Timothy A. Springer, Ph.D. <span class="Apple-converted-space"> </span><span class="Apple-converted-space"></span><span class="Apple-converted-space"></span></span></span><span class="Apple-converted-space"><span class="Apple-style-span" style="font-family: Arial; "></span></span><span class="Apple-converted-space"></span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Latham Family Professor of Pathology </span></span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Harvard Medical School <a href="http://idi.harvard.edu/springer">http://idi.harvard.edu/springer</a> </span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Immune Disease Institute <a href="mailto:springer@idi.harvard.edu">springer@idi.harvard.edu</a> </span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Program in Cellular and Molecular Medicine, Dept. Medicine</span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Div. Hematology Children's Hospital Boston</span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">3 Blackfan Circle, Rm 3103 phone: 617-713-8200 </span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Boston MA 02115 fax: 617-713-8232 </span></div><div style="font-family: Arial; "><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></span></span></div></span></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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<br><div><div>On Apr 29, 2011, at 1:40 PM, Paul Adams wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br>The Phenix developers are pleased to announce that version 1.7.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site:<br><br><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://phenix-online.org/download/">http://phenix-online.org/download/</a><br><br>Some of the new features in this version are:<br><br>Graphical Interface<br>-------------------<br>- New interfaces for: phenix.phase_and_build, phenix.mtz2map, phenix.french_wilson<br>- Updates to the Structure comparison GUI, which now allows use of non-identical sequences, <br> and results viewing in PyMol.<br>- A plugin for running multiple sequence alignment<br><br>Installers<br>----------<br>- Graphical installers for Macintosh (installs in /Applications)<br>- Binary installer for 64-bit Mac Intel (OS 10.6 only)<br><br>New Commands<br>------------<br>- phenix.french_wilson (new command):<br> - Implements French & Wilson correction of negative and weak intensities (see<br> Acta Cryst A34:517 [1978])<br> - outputs modified amplitudes in MTZ format<br> - used internally by default in Phaser GUI and phenix.refine when intensities<br> are provided<br>- phenix.reciprocal_space_arrays (new command):<br> - this tool takes a PDB model and a data file and outputs an MTZ file<br> containing a number of arrays that are typically used in various<br> crystallographic calculations, such as R-factors, maps, refinement targets, etc.<br> The output arrays include:<br> - Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, Hendrickson-Lattman<br> coefficients (input original, computed from model and combined),<br> FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more<br>- phaser.brunett (new command):<br> - automated molecular replacement using incremental exploration, with support for parallelization<br> - quick SSM-superposition-based LLG evaluation for alternative models for the same component<br> - "puzzle"-assembly of solutions for a more complete solution<br> - novel space group determination algorithm that retains possible space groups until they are <br> significantly outperformed by others<br> - handles custom models (used without modification), templates (a PDB template and an alignment, <br> Sculptor is run to create models from it) and homology searches (PDB and alignment obtained from<br> homology search, currently HHPRED and BlastXML; data downloaded from EBI)<br><br>Structure refinement<br>--------------------<br>- New output MTZ file that contains original data, amplitudes used in refinement, and map <br> coefficients (this replaces *_map_coeffs.mtz)<br>- French and Wilson procedure automatically applied if intensities are input to refinement<br>- Optional automatic rigid-body grouping by polymer chain (rigid_groups_mode=one_group_per_chain)<br>- Reference model uses a "top-out" restraint potential with a smooth cutoff<br>- Automatic determination of Saenger class for nucleic acid base pairs (if not provided by user)<br>- Ability to run phenix.find_tls_groups internally to obtain atom selections<br> - option: tls.find_automatically=True<br>- Automatic non-bonded distance correction for H-bonded atoms<br><br>Molecular Replacement<br>---------------------<br>- phenix.mr_rosetta:<br> - Bug fixes<br> - Added web site with data used in Nature Rosetta+Phenix paper at:<br> http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/<br> - Added keyword include_solvation_energy=False to allow use of mr_rosetta for membrane proteins.<br>- phenix.automr:<br> - bug fix in residue number input, now allows four-digit IDs<br><br>Ligands<br>-------<br>- eLBOW:<br> - Geometries can be generated using CSD Mogul substructure searches of<br> experimental geometries. Estimated standard deviations of the bonds<br> and angles are also included in the restraints file.<br><br>Visualization<br>-------------<br>- KiNG (phenix.king):<br> - Improved opening multiple electron density maps: tiered windows, with<br> automatic deciphering of file name to preset sigma levels and colors.<br> - Added -phenix command line option to preset map colors to be more like Coot.<br><br><br>For a full list of changes see:<br><br><span class="Apple-tab-span" style="white-space:pre"> </span>http://www.phenix-online.org/documentation/CHANGES<br><br>Please note that this publication should be used to cite use of Phenix:<br><br>PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunk�czi, 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).<br><br>Full documentation is available here:<br><br><span class="Apple-tab-span" style="white-space:pre"> </span>http://www.phenix-online.org/documentation/<br><br>There is a Phenix bulletin board:<br><br><span class="Apple-tab-span" style="white-space:pre"> </span>http://www.phenix-online.org/mailman/listinfo/phenixbb/<br><br>Please consult the installer README file or online documentation for<br>installation instructions.<br><br>Direct questions and problem reports to the bulletin board or:<br><br><span class="Apple-tab-span" style="white-space:pre"> </span>help@phenix-online.org and bugs@phenix-online.org<br><br>Commercial users interested in obtaining access to Phenix should visit the<br>Phenix website for information about the Phenix Industrial Consortium.<br><br>The development of Phenix is principally funded by the National Institute of<br>General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge<br>the generous support of the members of the Phenix Industrial Consortium.<br><br>-- <br>Paul Adams<br>Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab<br>Adjunct Professor, Department of Bioengineering, U.C. Berkeley<br>Vice President for Technology, the Joint BioEnergy Institute<br>Head, Berkeley Center for Structural Biology<br><br>Building 64, Room 248<br>Tel: 1-510-486-4225, Fax: 1-510-486-5909<br>http://cci.lbl.gov/paul<br><br>Lawrence Berkeley Laboratory<br>1 Cyclotron Road<br>BLDG 64R0121<br>Berkeley, CA 94720, USA.<br><br>Executive Assistant: Kathleen Moody [ KLMoody@lbl.gov ][ 1-510-495-2506 ]<br>--<br><br><br><br>_______________________________________________<br>phenixbb mailing list<br>phenixbb@phenix-online.org<br>http://phenix-online.org/mailman/listinfo/phenixbb<br><br></div></blockquote></div><br></body></html>