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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:
>
> [log in to unmask] and [log in to unmask]
>
> 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
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