Macs in Chemistry

Insanely Great Science

Pymol 2.0 released

 

The popular molecular visualisation application Pymol has been updated to version 2.0. This is a major update and the changes are detailed below.

You can either download a disk image (117 MB) or instal using Anaconda (Python 2.7)

conda install -c schrodinger pymol

screenshot4

Major Changes

  • Unified modern interface
  • PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms
  • Anaconda Python distribution
  • Better third-party plugin and custom scripting support
  • Open access incentive executables with new licensing mechanism

New Features

  • Native retina resolution / 4k display support
  • Dock/undock and rearrange certain panels (Builder, Feedback Browser, Volume Editor)
  • Support for trackpad gestures (pinch for zoom in/out, z-rotate)
  • Dedicated dialogs for opening MAE files, MTZ files, maps and trajectory files
  • New APBS Plugin panel
  • .pymolrc script editor with syntax highlighting
  • Properties editor
  • Improved Draw / RayTrace dialog
  • MPEG-4 and GIF movie export panel
  • Excel exporter plugin (Windows and Mac)
  • Open files by dragging from file browser to PyMOL window
  • wire and licorice representation aliases for combined lines/nonbonded and sticks/nb_spheres
  • New commands: “copy_to” and “uniquify”
  • Single-letter code labels (“label oneletter”)
  • Label Wizard menus for colors and transparency
  • Improved file types registration on Windows (Setting > Register File Extensions)

Settings changes

  • Changed default values for several settings:
  • opaque_background=off
  • cartoongapcutoff=10
  • autoshowclassified=1 (=3 for > 500k atoms)
  • valence=on
  • stickhscale=0.4
  • smoothsurfaceedges=on

Menu changes

  • “Open Recent” file menu
  • File > New Window opens new PyMOL window
  • Setting > Register File Extensions
  • Plugin > Legacy Plugins
  • New > Pseudoatom > Callout
  • A > Copy to object
  • A > State > Split

Bug fixes

  • Fixed slow performance of “extract” command
  • Better unicode/UTF-8 handling
  • Fixed inconsistent look of labels and connectors on Retina and non-Retina displays
  • Fixed labelrelativemode=2 raytracing
  • Improved Maestro and MOE format compatibility
  • Fixed internal GUI clipping on certain Windows systems with integrated Intel graphics

The new user interface and all core improvements will be pushed to the open source SVN repository early next year.


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Predicting sites of metabolism Vortex script

 

It is really useful to have two sites of metabolism tools available that use contrasting methodologies, FAME 2 using curated dataset of experimentally determined metabolism data to build a machine learning model using simple descriptors. In contrast SMARTCyp uses precomputed activation energies from density functional theory (DFT) calculations of model compounds.

I previously wrote a script displaying the [results of a SMARTCyp calculation in a webview. The first part of the script imports the smartcyp.jar, however with each update I was finding issues so I thought it might be better to simply treat SMARTCyp as a command line application and use subprocess to access it.

Using a similar script we can also access FAME2

More details here.

somprediction


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Xcode 9.0 is available for download

 

The new version of Xcode is available for download. Xcode 9.0 includes Swift 4 and SDKs for iOS 11, watchOS 4, tvOS 11 and macOS High Sierra 10.13.

  • The source code editor has been completely rebuilt for amazing speed. It scrolls at a constantly smooth rate, no matter the files size, also supports Markdown.
  • Refactoring to easily select and modify structure of code
  • Swift 4 compiler can also compile Swift 3 to aid transition
  • Xcode 9 makes working with source control – and with GitHub – easier and more tightly integrated.
  • Simulator app updated.

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chemfp 1.3 released

 

Chemfp is a set of command-line tools and a Python library for working with cheminformatics fingerprints. It can use OEChem/OEGraphSim, RDKit, or Open Babel to create fingerprints in the FPS format, and it implements a high-speed Tanimoto search.

The software is available under the MIT license. For more information see http://chemfp.com/. Documentation is available from http://chemfp.readthedocs.io/en/chemfp-1.3/ .

There are many changes over chemfp 1.1, which was the last release of the public/no-cost version of chemfp. The biggest ones are:

  • Tested against the current version of all of the toolkits

  • Added support for the Avalon and pattern fingerprints in RDKit

  • In-memory Tanimoto searches for 166-bit MACCS keys on computers with the POPCNT instruction is about 30% faster.

  • FPS loading is about 40% faster. As a result, file-based searches are about 25% faster.

  • The in-memory search algorithms in version 1.1 were parallelized with OpenMP, but the NxM k-nearest search was left out. That case is now also parallelized.

  • Some of the APIs from the commercial version were backported to 1.3, including the fingerprint writer API and functions for substructure fingerprint screening.

  • Added and improved docstrings

This release support Python 2.7 but it no longer supports Python 2.5 or Python 2.6. The commercial version supports Python 2.7 and Python 3.5+, handles more than 4GB of fingerprint data, and has a binary fingerprint format for fast loading.

It is available from http://dalkescientific.com/releases/chemfp-1.3.tar.gz.


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GROMACS 2016.4 has been released

 

Molecular dynamics simulation in general, and GROMACS in particular, has made it possible to study large and complex biomolecular systems such as membranes and membrane proteins and probe atomic detail that is not accessible to any experimental methods. GROMACS can already use thousands of cores and hundreds of accelerators efficiently in parallel, even for a single quite small system. When adding ensemble-level parallelization with Copernicus the total problem scaling extends another two orders of magnitude.

These release notes document the changes that have taken place in GROMACS since version 2016.3 to fix known issues. It also incorporates all fixes made in version 5.1.4 and several since.

  • Fixes where mdrun could behave incorrectly
  • Disabled PME tuning with the group scheme
  • Fixed value of Ewald shift
  • Fixed orientation restraint reference
  • Fixed bugs with setup for orientation restraints
  • Worked around missing OpenMP implementation in orientation restraints
  • Enable group-scheme SIMD kernels on recent AVX extensions
  • Fix FEP state with rerun
  • Fixed COM pull force with SD
  • Fix PBC bugs in the swap code
  • Fixed flat-bottomed position restraints with multiple ranks
  • Fixed null pointer print in DD
  • Improved the “files not present” error message
  • Fixed LJ-PME + switch grompp error
  • Fixed unused SIMD PME table kernel
  • Fixed bugs in most double-precision Simd4 implementations
  • Avoid inf in SIMD double sqrt()
  • Fix NVML error messages
  • Fixed IMD interface malfunctions
  • Fixed initial temperature reporting
  • Fix exception in SIMD LJ PME solve
  • Fixes for gmx tools
  • Fixed memory access issues in gmx solvate
  • Fixed a consistency check in gmx make_edi for flooding
  • Supported quiet trajectory-handling I/O
  • Improved documentation
  • Migrated much content from the wiki to the user guide
  • Corrected the PDF manual to reflect that all tools are called gmx
  • Clarified gmx editconf help text
  • Added missing .mdp file documentation for the enforced rotation module
  • Fixed parameter description for dihedral_restraints
  • Replaced instance of “group” by “coord” in pull .mdp documentation
  • Portability enhancements
  • Supported CUDA 9/Volta for nonbonded kernels
  • Really enabled AVX512 in the GROMACS-managed build of FFTW
  • Fixed aspects for compiling and running on Solaris
  • Fixed AVX512F compiler flags
  • Fixed compiler flags for using MKL
  • Fixes compilation issues with ARM SIMD

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