Macs in Chemistry

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crystallography

OpenEye announces the release of AFITT v2.4.1.

 

AFITT is a crystallographic tool for correctly placing small molecules in real-space density. AFITT merges OpenEye’s Shape and MMFF technologies into a new combined forcefield that fits small molecules into crystallographic density while maintaining excellent chemistry.

Support has been added for Ubuntu 16, OSX 10.10, OSX 10.11, and OSX 10.12. OSX 10.7, OSX 10.8, OSX 10.9, SuSe 11, and Redhat 5 x86 are no longer supported

This release adds support for Coot 0.8. Coot 0.6 and earlier versions are no longer supported.

FLYNN (the ligand fitting application) comes bundled with a refinement dictionary writer, WRITEDICT, that uses the MMFF94 force field to derive geometrical constraints for input ligands or protein-ligand complexes. The output dictionaries enforce, as closely as possible, the input ligand’s geometries while allowing the refinement programs to modify the geometry as needed. This version corrects a serious error in which WRITEDICT wrote incorrect bonds lengths for 5-5, 5-6 heterocycle ring systems. A bug that caused PDB remark data that was more than 72 characters long to be clipped from the refined output has been fixed. This only occured when the input and output file formats were both PDB.


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USPEX Universal Structure Predictor

 

I've added USPEX Universal Structure Predictor: Evolutionary Xtallography to the alphabetical listing of applications

A.R. Oganov, J.C. Schon, M. Jansen, S.M. Woodley, W.W. Tipton, and R.G. Hennig. Appendix: First Blind Test of Inorganic Crystal Structure Prediction Methods, pages 223–231. Wiley-VCH Verlag GmbH & Co. KGaA, 2010.


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CrystalMaker Updates

 

The suite of software to support crystallography has been updated

CrystalDiffract brings the world of x-ray & neutron powder diffraction to your computer.

CrystalMaker is the easiest way to build, visualize and understand structures of crystals and molecules

CrystalViewer a free viewer offers high-quality graphics, plus distance and measurement tools, multi-touch control (Mac) and the ability to view crystal lattices along specific lattice vectors or plane normals. 3D Printing Support - save any displayed structure as an STL file, as supported by most 3D printers.

visualization-link


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CCP4 released

 

The current version is CCP4 7.0 (07 January 2016). The new packages include:
SHELX suite: co distribution for academic users
CCP4I2: new ccp4 interface
DIALS: data processing and integration
ARCIMBOLDO-LITE: molecular replacement pipeline
The updated packages include PHASER, XIA2, REFMAC, MONOMER LIBRARY, AMPLE, COOT, AIMLESS POINTLESS, CTRUNCATE, DIMPLE, BLEND and many more

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

The latest version supports Mac OSX and Linux and requires X11. Source code is also available.

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Mac OSX installer for Coot

 

A reader sent me a link to a posting on the brilliant Crystallography on OS X website highlighting the availability of a stand alone version of Coot for Mac OSX

With considerable help from Nat Echols, we can now build coot automatically every night a new revision is available. I have two versions, built on two different computers. The 10.6 version should run on 10.6.8 or greater. The 10.9 version is for 10.9 or later.. The package installer will install everything in /Library/Coot. Unfortunately, it breaks if you move it. A wrapper shell script called "coot" will reside in /usr/local/bin/coot when you are done.

Coot (Crystallographic Object-Oriented Toolkit) is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.

I've also added a link on the Spectroscopy page.

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DiffPy

 

DiffPy - Atomic Structure Analysis in Python A free and open source software project to provide python software for diffraction analysis and the study of the atomic structure of materials.

diffpy

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EnCIFer for CIF validation

 

The Crystallographic Information File (CIF) is the internationally agreed standard file format for information exchange in crystallography. The CIF standard is supported, maintained and developed by the International Union of Crystallography (IUCr) and most major journals require electronic data depositions in CIF format. enCIFer enables users to validate CIFs and ensure their files are format-compliant for deposition with journals and databases or for storage in laboratory archives. enCIFer should also be used to add information safely to CIFs without corrupting the strict syntax. enCIFer operates on single or multi-block CIFs allowing you to:

  • Identify and correct syntax/format violations
  • Safely edit information to your CIF without corrupting the strict syntax, for both single data items and data loops
  • Supplement the data in your CIF via two data entry wizards, one for publication details and the other for chemical, physical and crystallographic properties
  • Select from a choice of CIF dictionaries and check against a user-customisable list of mandatory data items
  • Visualise structure(s) in a CIF, including displacement ellipsoids

Requires Mac OS X: 10.6, 10.7, 10.8, 10.9

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AFITT v2.3 has been released

AFITT v2.3 has been released

AFITT merges OpenEye’s Shape and MMFF technologies into a new combined forcefield that fits small molecules into crystallographic density while maintaining excellent chemistry. The AFITT GUI also provides an interface to external refinement programs and tools to validate the refinement including interactive Ramachandran plots and real-space correlation coefficient calculation.

ENHANCEMENTS:

  • PM3/AM1 semi-empirical quantum force field support
  • Better density detection, especially for poor ligand density
  • Optimization enhancements for high-strain ligands
  • (AFITT-GUI) – Protein side-chain fitting (not enabled by default)
  • (AFITT-GUI) – Hydrogen bond visualization (on by default)
  • (AFITT-GUI) – Conflicts with default dictionaries (CCP4) visualized
  • (AFITT-GUI) – Speed improvements in wizard navigation
  • (AFITT-CL) – More control on report and logging generation



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CrystalMaker 8.7.1 released

CrystalMaker 8.7.1 has been released.

CrystalMaker is a program for building, displaying, manipulating and animating all kinds of crystal & molecular structures now with support for colour 3D graphics and multi structure animation.

crystalmaker

From the release Notes:-

  • Indexed Online Help. The online help system is now indexed. Users can search for terms in the Help menu's search box, and a list of appropriate topics is displayed in the menu.
  • Miscellaneous Changes. This version includes miscellaneous bug fixes and a workaround for system changes on OS X "Lion" and "Mountain Lion": Fixed a spurious "Failed to read XYZ file" warning that was displayed when a generic text file was read into the program. (The correct structure was invariably plotted, but the alert was incorrect). The Edit Annotation palette's "Scalebar" formatting buttons are now displayed correctly (this fixes an error introduced in the previous version). The Video Recorder palette now correctly resets the movie size to zero, before recording another video. Added a workaround for changed toolbar behaviour in OS X "Lion" and "Mountain Lion". Toolbar visibility is again correctly saved in the Preferences file. Fixed a potential problem with the File > Open Recent submenu, which could cause the command to fail.



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Added pycifrw to spectroscopy page

PyCIFRW provides support for reading and writing CIF (Crystallographic Information Framework) files using Python. PyCIFRW is written entirely in Python. While this makes parsing of large CIF files rather slow, it will run wherever Python runs.

Now added to the spectroscopy page

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Added Motofit to alphabetical listing

Motofit co-refines Neutron and X-ray reflectometry data, using the Abeles matrix / Parratt recursion and least squares fitting (Genetic algorithm or Levenberg Marquardt). It works in the IGOR Pro environment (TM Wavemetrics).

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AFITT v2.2.0 has been released

OpenEye have announced that AFITT v2.2.0 has been released.  This is the first release of the AFITT GUI that fully supports fragment and cocktail fitting to crystallographic data.  In addition, poses fit to density can be re-ranked based on various docking scores (PLP, Chemscore) as well as the Real Space Correlation Coefficient (RSCC).  This is particularly useful when analyzing highly symmetric ligands that can be fit to density equally well with multiple poses.

AFITT is an application designed to help crystallographers fit ligands to observed data.  Ligands are placed in density and optimized in real-space limiting molecular strain thereby producing excellent matches to density while preserving known chemistry

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J-ICE a Jmol Interface for Crystallographic and Electronic Properties.

J-ICE is a Jmol Interface for Crystallographic and Electronic Properties. Read More...
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CrystalMaker Update

The Apple design award winning CrystalMaker has been updated Read More...
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CrystalMaker Update

CrystalMaker adds much improved 3D graphics in major update. Read More...
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PSILO Macromolecular Database

PSILO is a database system that provides a repository for macromolecular and protein-ligand structural information. Read More...
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Cambridge Structural Database, Mercury available

Mercury CSD version 2.0 is now available from the Cambridge Structural Database. Read More...
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CrystalEye

The aim of the CrystalEye project is to aggregate crystallography from web resources. Read More...
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