Chemical structure drawing is very much dominated by a couple major applications so it is nice to see an alternative being made available. MoleculeSketch is a simple and easy to use drawing App for chemical formulas and reactions. New macOS version 2.3 and iPad version 2.1 have just been released.
It has following features:
- add atoms and bonds nicely by position locking (can be disabled)
- choose different double bond styles
- add stereo bonds
- add bonds with higher hapticity
- type functional groups by double-clicking on symbol
- show missing hydrogen atoms depending on free valences
- "grow" and remove hydrogen atoms
- show non bonding electron pairs on heteroatoms
- change background color of drawing area and add a grid
- copy/paste/cut molecules and drawings
- paste drawings into other applications as pdf drawing
- import from mol files (V2000 format)
- use trackpad gestures for zooming and rotation
- access drawing attributes from popover panels
- add reaction arrows and text fields
- calculate average mass and formula of molecules
- group and arrange objects
Just got a message that VESTA has been updated to version 3.4.8 with several bug fixes, support for dark mode, and Improved support for pdb file format.
VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Some of the novel features of VESTA are listed below.
- Deal with multiple structural models, volumetric data, and crystal morphologies in the same window.
- Support multiple tabs corresponding to files.
- Support multiple windows with more than two tabs in the same process.
- Deal with virtually unlimited number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces (theoretical limit on 32bit operating system is 1,073,741,823)
- Support lattice transformation from conventional to non-conventional lattice by using matrix. The transformation matrix is also used to create superlattice and sublattice.
- Visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP.
- Transparent isosurfaces can be overlap with structural models.
- Isosurface can be colored on the basis of another physical quantity.
- Arithmetic operations among multiple volumetric data files.
- High quality smooth rendering of isosurfaces and sections.
- Export high-resolution graphic images exceeding Video card limitation.
iRASPA: GPU-accelerated visualisation software for materials scientists
Just came across this application and I thought it would be worth flagging, iRASPA is a GPU-accelerated visualization package aimed at material science. Molecular Simulation Journal. 44 (8): 653–676 DOI
iRASPA is a visualization package (with editing capabilities) aimed at material science. Examples of materials are metals, metal-oxides, ceramics, biomaterials, zeolites, clays, and metal-organic frameworks. iRASPA is exclusively for macOS and as such can leverage the latest visualization technologies with stunning performance. iRASPA extensively utilizes GPU computing. For example, void-fractions and surface areas can be computed in a fraction of a second for small/medium structures and in a few seconds for very large unit cells. It can handle large structures (hundreds of thousands of atoms), including ambient occlusion, with high frame rates.
Via iCloud, iRASPA has access to the CoRE Metal-Organic Frameworks database containing 4764 structures and 2932 structures enhance with atomic charges. All the structures can be screened (in real-time) using user-defined predicates. The cloud structures can be queried for surface areas, void fraction, and other pore structure properties.
iRaspa is written in Swift.
Resuts from Avogadro Survey
The results of the Avogadro 2018 Community Survey are now in.
Avogadro is an advanced 3D molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
The results are well worth browsing though but here are a few things I've picked out
- The most common way people hear about Avogadro by word of mouth.
- Most people install downloaded binaries
- Many users can code, mainly Python
- Most tasks performed centre around initial molecule building and editing
You can download from sourceforge here https://sourceforge.net/projects/avogadro/files/latest/download