-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Paul,
thank you for the answer. I was curious, especially since there was a recent paper on anomalous phasing with neutron scattering (doi:10.1038/srep31487), and wondered if this was related. I also appreciate seeing development in neutron crystallography. Best, Tim On Wednesday, November 02, 2016 03:01:03 PM Paul Adams wrote: > Hi Tim, > > you are correct as it is scattering by the nucleus. Support for ions means > that users can use an “ion name”, e.g. Ca+2 for an atom and the appropriate > scattering factors will be used. The neutron scattering table previously > didn’t include the ionic names. > > Cheers, > Paul > > > On Nov 2, 2016, at 2:41 PM, Tim Gruene <tim.gru...@psi.ch> wrote: > > > > -----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----- - -- - -- 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 iD8DBQFYGsQlUxlJ7aRr7hoRAmckAJ9Gfob7pHduqI5qg4bDbs/OVmv8+ACcCTDe 2ZUcGuov2PQH7wK77xraCXo= =E93A -----END PGP SIGNATURE-----
