-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Paul,
I am surprised by the mentioning of support for ions in the neutron scattering tables. Would you have a reference? I always though neutron scattering was independent of the electronic state of an atom. Best, Tim On Wednesday, November 02, 2016 12:04:55 PM Paul Adams wrote: > The Phenix developers are pleased to announce that version 1.11.1 of Phenix > is now available (build 1.11.1-2575). Binary installers for Linux, Mac OSX, > and Windows platforms are available at the download site: > > http://phenix-online.org/download/ > > Highlights for this version: > > New tools for omit maps without bulk solvent in omitted region, automated > sharpening of cryo-EM and crystallographic maps, and segmentation of maps. > Improved NCS search. New automated model-building tools for low-resolution > maps - especially cryo-EM, tools for matching chains (both residues and > direction), multiple improvements to phenix.real_space_refine and addition > of new GUI. Improved model geometry restraints, many improvements to > Phaser, improved validation incorporating new MolProbity features, > simplified Rosetta installation, improved support for Amber, updated > dependencies, Unicode support in GUI, new unified interface for atom > selections. > > - General > - Improved geometry restraints: > - Conformation-Dependent Library for omega added (omega_cdl=True) > - Installation > - Rosetta installation centralised for phenix.rosetta_refine, > phenix.mr_rosetta and ERRASER > - Improved NCS search procedure with simplified parameters. Provides > status of user-supplied NCS groups during validation > (refused/modified/ok) - Updated dependencies > - biopython 1.64 -> 1.66 > - sphinx 1.2.2 -> 1.4.4 > - ipython 2.1.0 -> 3.2.1 > - pip 6.0.7 -> 8.0.2 > - Neutron scattering tables: support ions > > - Amber refinement > - Alpha release dev-2203 > > - GUI > - New interfaces > - phenix.map_comparison > - phenix.polder > - phenix.structure_search > - phenix.real_space_refine > - New selection editor > - Unified interface for selecting atoms > - Secondary structure annotations > - NCS groups > - TLS groups > - Refinement strategy options > - Unicode support > - Non-ASCII characters are supported for most fields (e.g. file paths > and job titles) > - Using non-ASCII characters in projects/jobs will prevent earlier > versions that do not have Unicode support from opening the project list > correctly - Migrated validation after phenix.refine to use regular > MolProbity for consistency (older versions of Phenix will not open new > jobs) > - phenix.real_space_correlation can now accept map files > - phenix.molprobity can now accept map files > - Updated dependencies for Linux > - libpng 1.2.52 -> 1.5.26 > - freetype 2.4.2 -> 2.6.3 > - gettext 0.18.2 -> 0.19.7 > - glib 2.12.11 -> 2.46.2 > - expat 1.95.8 -> 2.1.0 > - fontconfig 2.3.95 -> 2.11.1 > - render 0.8 -> 0.11.1 > - xrender 0.8.3 -> 0.9.7 > - xft 2.1.2 -> 2.3.2 > - pixman 0.19.2 -> 0.34.0 > - cairo 1.8.10 -> 1.14.4 > - pango 1.16.1 -> 1.38.1 > - atk 1.9.1 -> 2.18.0 > - libtiff 3.6.1 -> 4.0.6 > - gtk+ 2.10.11 -> 2.24.29 > - matplotlib 1.3.1 -> 1.5.1 > > - Maps > - phenix.polder calculates omit maps which exclude the bulk solvent around > the omitted region. This way, weak densities possibly obscured by bulk > solvent may become visible. > - phenix.model_map: Given PDB file calculate model map and output as CCP4 > formatted binary map file. > - phenix.mask: Given PDB file calculate bulk-solvent mask and output as > CCP4 formatted binary map file. > - phenix.auto_sharpen: Optimizes resolution dependence of a map to improve > clarity > - phenix.segment_and_split_map: Carries out segmentation of a map > > - Model-building > - phenix.map_to_model builds models in low-resolution maps > - builds any combination of RNA/DNA/protein > - if NCS present, builds the asymmetric unit of NCS and expands > to the entire map > - phenix.segment_and_split_map breaks up a map into the asymmetric > unit of NCS and further subdivides that into contiguous regions > of density > - phenix.chain_comparison compares CA or P atoms of two models and > identifies how many residues match and how many are in the same > direction > > - phenix.real_space_refine: > - Support output of refined model in mmCIF format > - ADP refinement runs by default at the last macro-cycle. Several CPUs can > be used to speed up refinement: use nproc=NUMBER_OF_CPUs parameter for > this. > > - phenix.model_idealization: tool to idealize model geometry while staying > as close as possible to the starting model. Currently proteins only. > Idealize covalent geometry and secondary structure, as well as eliminate > rotamer and Ramachandran plot outliers, C-beta deviations. > > - phenix.geometry_minimization > - ability to use reference torsion restraints > - ability to use NCS constraints > > - phenix.phaser > - SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP > peak lists - selection by CHAIN and MODEL for PDB coordinate entry > - automatic search number for single search ensemble > - packing 'trace' molecule can be entered independently of coordinates > and map - read TNCS/anisotropy binary files to avoid refinement, when > running through scripts - write tNCS and anisotropy parameters to binary > files (non-python interface) - default reading of I (or failing that, F) > from mtz file (LABIN optional) - trace for ensembles from maps = hexgrid of > 1000+/-100 points > - trace for ensembles from coordinates above 1000 Calpha = hexgrid of > 1000+/-100 points - trace for ensembles from coordinates twixt 1000 atoms > and 1000 Calpha = Calpha atoms - trace for ensembles from coordinates under > 1000 atoms = all atoms - packing by pairwise percent only, other packing > modes obsoleted - packing test during FTF run by default with 50% pairwise > packing cutoff - automatic tNCS NMOL determination in presence of > commensurate modulation - added MODE GIMBLE, which splits ensembles by > chain for rigid body refinement - support for unicode > - solution coordinates placed nearest to input coordinates if possible > > - phenix.reduce > - Updated reduce_wwPDB_het_dict as of Aug 12, 2016 > - New script for updating het dict > - Reduce no longer rotates methionine methyls by default. -DOROTMET flag > reinstates old behavior > > - phenix.ramalyze > - Improved handling of residue connectivity > - Summary statistics provided for altloc A specifically where multiple > altlocs present > > For a full list of changes see: > > http://www.phenix-online.org/documentation/CHANGES > > 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: > > h...@phenix-online.org and b...@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 Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iD8DBQFYGl2CUxlJ7aRr7hoRAiR+AKDIH3tEU2YHL479eIO5eX6woWbWWACgpGik 8fW+W5o3D05fH6mGT0+rxvo= =qDPr -----END PGP SIGNATURE-----
