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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 <[log in to unmask]> wrote:
> >
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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
> >
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- --
- --
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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