Just got this message
We are pleased to introduce version 6.6 of our ChemDoodle 3D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $15, and we have a free trial available at: https://www.chemdoodle.com/3d
Major new features include the ability to perform full scene modeling simulations, an implementation of the FIRE optimizer, 3D molecular structure alignment, improved bond deduction with new bond order perception algorithms, and more.
News just in from ChimeraX team https://www.rbvi.ucsf.edu/chimerax/data/czi-nov2021/apple_m1.html.
We are making a version of our ChimeraX molecular graphics program that runs natively on Apple's new M1 CPUs for faster interactive calculations. We'll report some speed-up timings and describe difficulties porting from Intel to the Apple M1 CPU. A native Apple M1 version of ChimeraX is not yet available, but we expect to release it within 6 months.
Difficulties porting ChimeraX to Apple M1 CPUs
- ChimeraX Python and C++ code needs no changes.
- ChimeraX uses 90 packages developed by others.
- 60 are pure Python from the PyPi repository.
- 30 are binary packages that need Apple M1 versions.
- 6 binary packages do not have Apple M1 distributions: ambertools, h5py, imagecodecs, netcdf4, pytables, scipy.
- Qt 6 window toolkit is distributed for Apple M1 but not Qt 5.
- ChimeraX uses Qt 5, the stable Qt version from 2012 - 2021.
- Qt 6 with html support was released September 2021.
- Apple M1 applications must be either all native M1 binaries or all Intel binaries, no mixing.
- Need to distribute either a large univeral package that includes both Intel and M1 binaries, or two separate ChimeraX versions.
Potential advantages of native Apple M1 ChimeraX
- Better OpenGL driver stability with Apple M1 GPU.
- No graphics driver crashes among 43 ChimeraX bug reports in 2021 with Apple M1.
- About 100 ChimeraX graphics driver crashes reported on Intel Macs in past 2 years.
- Better C++ crash stack traces with native M1 app than with Intel emulation.
- Intel ChimeraX crashes on M1 often give no C++ stack trace.
ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from https://www.rbvi.ucsf.edu/chimerax/
Updates since version 1.3 (Dec 2021) include:
- search/retrieve from EBI AlphaFold DB 3rd release, ~1 million structures
- display AlphaFold predicted aligned error (PAE) plots
- can BLAST UniRef100,90,50 (+ previous choices AlphaFold, PDB, NR)
- AlphaFold prediction of multimers (of limited size) on Google Colab
- independent centers of rotation available as mouse mode
- join models with Build Structure tool or command
- define axes for display and/or use in measurements
- increase/decrease VDW radii relative to their current values
- switch PDB residue numbering scheme (author/canonical/uniprot)
- align sequences with Clustal Omega or MUSCLE
- calculate % identity in sequence alignments
- window toolkit updated to Qt 6.2.3 from 5.15.2
There is a ChimeraX workshop here https://youtu.be/M2K72Kgk718.
An interesting update to the popular 3D molecule viewer Chemdoodle 3D.
ChemDoodle 3D v6.2 introduces advanced and customizable anaglyph support for augmented reality (AR) right on your computer. Now you can fully visualize the 3D molecules you are building in 3D! If you have red-cyan anaglyph glasses, you will see the above image in 3D.
There are a choice of glasses on Amazon, ranging from inexpensive plastic and card Cyan/Red/Blue 3D Glasses to more durable plastic 3D glasses there are also Clip-On for Wearers of prescription glasses
In addition to the classic red-cyan glasses, green-magenta and amber-blue glasses are supported as well.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. However, it still lacks a graphical user interface (GUI) for molecular manipulations when doing some modeling tasks.
A recent publication DOI describes work using the Tcl/Tk toolkit to develop a user-friendly GUI for VMD, named Molcontroller.
All the scripts and installation instructions are available https://github.com/ChenchenWu-hub/Molcontroller.
UCSF ChimeraX is the next-generation visualization program from the Resource for Biocomputing, Visualization, and Informatics at UC San Francisco.
The image below shows the COVID-19 MPro with a fragment bound taken from Project Moonshot.
The release candidate is available here https://www.rbvi.ucsf.edu/chimerax/download.html.
chimerax-rc.dmg built: 2020-09-07 04:36:35 PDT committed: 2020-09-06 22:34:34 PDT size: 337.3 MiB
Download is a disk image containing the application. Tested on macOS 10.13. This application does not run on 10.12 or older due to operating system changes.
I just noticed that the latest update to iBabel has now been downloaded over 500 times.
iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel described in an article in J Cheminformatics, Open Babel: An open chemical toolbox DOI. iBabel was originally written as an AppleScript Studio application which underwent several updates, but gradually became unsupportable. So rather than try to patch the AppleScript Studio/ApplescriptObjC application I decided on a starting afresh with a complete rewrite using Cocoa/Swift to take advantage of new technologies, this has meant some features have been lost, some new ones added but hopefully the core features are still there.
Instructions for download and installing are on the main iBabel page, remember you need to install OpenBabel first.
There is a new test build of VMD for Catalina.
Latest version (May 8) Updated modeling plugins updated for Tk 8.6 (grid vs. pack corrections)
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
There are details of many other scientific applications under Catalina here
PyMOL 2.4 has been released. Download ready-to-use bundles from https://pymol.org/ or update your installation with
conda install -c schrodinger pymol
Incentive PyMOL only:
- Support for https://lookingglassfactory.com/schrodinger
- Pi-Pi and Pi-Cation interactions (A > find > pi-interactions)
- WaterMap result presets (A > preset > WaterMap ...)
- APBS Plugin improvements (multi-state assemblies, propka pH calculation)
Open-Source and Incentive PyMOL:
- Distinguish .mrc and .ccp4 formats (origin interpretation)
- Trajectory handling improvements
- Improved error handling in Python API with exceptions
- ... many bug fixes
This will be the last release with support for Python 2.7.
Full release notes https://pymol.org/dokuwiki/?id=media:new24
A minor update to iBabel Currently when you use the Viewer tab to display molecules only a 2D display is available as shown below.
However, now there are a couple of radio buttons below the image that can be used to choose either a 2D viewer or 3D viewer, this should be particularly useful when looking at the conformation of docked ligands. It should be noted that this does not actually generate a 3D structure it merely displays the input file using a 3D viewer 3Dmol.js if the file only contains 2D coordinates a 2D structure will be displayed.
You can read more and download iBabel here.
At the start of 2020 I decided that I'd try learning to program in Swift using Xcode, my first project was molSeeker a tool for searching online resources using chemical identifiers. This was really just a vehicle for me to learn Swift and now I'm delighted to be able to release a more substantial effort, a complete rewrite of iBabel.
iBabel is a graphical user interface (GUI) to the open-source cheminformatics toolkit Open Babel described in an article in J Cheminformatics, Open Babel: An open chemical toolbox DOI. iBabel was originally written as an AppleScript Studio application which underwent several updates. However, recent changes have made this unsupportable so I decided on a complete Cocoa/Swift rewrite.
You can read all about the new version of iBabel here including the links to the download. I've attached a couple of screenshots to give you an idea of what functionality is available.
File Conversion Tools
Viewing Molecule Files
Extension of molSeeker
iBabel 4.0 is freely available for download.
The latest update to SAMSON 2020, the open molecular modelling platform is now available.
This update brings one feature that I'm many having been asking for.
- Molecular builder, you can build molecules by adding individual atoms or by adding Assets, an assets can be anything: rings, fragments, radicals, whole molecules, proteins, nanoparticles, 2D materials, etc.
- Tooltips, Hovering nodes now displays information about them and their ascendants.
- Tutorials, SAMSON now contains step-by-step Interactive tutorials that guide you through SAMSON’s features at your own pace.
- The SAMSON API has been upgraded to expose the new functionalities of this release and let developers create fantastic molecular modelling experiences that they can distribute on SAMSON Connect.
SAMSON itself is free, and so are many SAMSON Elements (extensions). For non-free extensions, it essentially works like Netflix. Monthly and yearly subscriptions are available, with lower prices for academia (typically 60% off). Users subscribe directly online at https://www.samson-connect.net. When they need group or site licenses, they contact us at firstname.lastname@example.org for quotes.
There are Elements for conformational analysis, docking, molecular dynamics, crystal creator, molecular optimisation, protein alignment and much more.
Create your own elements
It's also possible to use python: https://documentation.samson-connect.net/scripting-guide/.
The core of SAMSON is not open source, but developers can do what they want with their modules (give their source or not), and the source of some of the modules are available on Github at https://github.com/SAMSON-Connect.
There is much more on Github https://github.com/1A-OneAngstrom/SAMSON-Developer-Tutorials.
The PDB in Europe have just introduced a new viewer for biomolecules, Mol*, is a new 3D molecular viewer developed in collaboration between RCSB PDB, PDBe, and CEITEC, from RCSB PDB and PDBe pages.
On the PDBe pages, Mol* has now replaced the LiteMol viewer in all instances, including on the PDBe search and entry pages e.g. pdbe.org/5lnk/3d. Access Mol* from any 3D View tab for Structure Summary pages at RCSB.org. Both the LiteMol and NGL viewers at PDBe and RCSB PDB, respectively, will no longer be actively developed.
Here is the structure of Aldehyde Oxidase PDB ID 4uhw.
ModelAR is a powerful 3D modeling tool for students looking to practice organic chemistry. You can explore chemical structures by creating a molecule on the workspace and quickly toggle to pop into AR. This Augmented Reality feature allows you to interact with virtual molecules in real space. ModelAR brings chemistry to life.
A reader recently pointed out BlendMol part of a suite of software tools developed by the Jacob Durrant Lab.
BlendMol is a Blender plugin that can easily import VMD 'Visualization State' and PyMOL 'Session' files. BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with popular analysis programs (i.e., VMD/PyMOL). Users can import into Blender the very molecular representations they set up in VMD/PyMOL.
This looks like a very interesting open-source project available on GitHub, however looking at the software page https://durrantlab.pitt.edu/durrant-lab-software/ I see there are a number of other interesting packages.
Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.
Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.
Scoria is a Python package for manipulating three dimensional molecular data. Unlike similar packages, Scoria is written in pure Python and so requires no dependencies or installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g., NumPy, SciPy, MDAnalysis), if present, to speed and extend its own functionality.
Looks like a great resource.
At the latest Bio-ITWorld 3decision was recognised with an award
3decision – next generation structural knowledge management solution
Although wildly used, rational structure-based drug design (SBDD) techniques are far from being applied to their fullest potential. The major hurdles lie in the inconsistent data persistence and the complexity of analyzing structural data. Moreover, the structural data is often analyzed by domain experts only and their knowledge and experience are not well shared and exposed to other communities. Abbvie has addressed these pitfalls by co-developing a web-based structural knowledge management solution called 3decision. It allows Abbvie to transform a massive amount of data coming from in-house and public 3D structures and sequences, into applicable knowledge for drug discovery projects. The collaborative aspects within SBDD projects are in focus and the user interface allows all types of users to easily generate, test and connect their ideas with each other. The development of 3decision allowed Abbvie to dramatically increases the ROI of SBDD work and protein structure production.
3decision is a web-based collaborative platform for storing, analyzing and sharing protein-ligand structures, sequences, and associated data, it works fine on a Mac and Google Chrome is recommended browser
Structure displayed using 3Dmol.js.
|Movement||Mouse Input||Touch Input|
|Rotation||Primary Mouse Button||Single touch|
|Translation||Middle Mouse Button or Ctrl+Primary||Triple touch|
|Zoom||Scroll Wheel or Second Mouse Button or Shift+Primary||Pinch (double touch)|
You might also be interested in these pages
Just got this message
We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://pymol.org/2/ or update your installation with "conda install -c schrodinger pymol". New features include: - Atom-level cartoon transparency - Fast MMTF export - Sequence viewer gaps display
This is the first time there are PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them.
Full release notes are here https://pymol.org/dokuwiki/?id=media:new23 and
I've mentioned Samson a couple of times and I noticed that the documentation has been updated. Documentation is a critical but often overlooked feature of software.
SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems
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.
The use of augmented and virtual reality in chemistry is slowly starting to gain traction. The initial use of virtual reality in drug discovery is well documented but usually confined to highly specialised hardware which has limited it's exposure to a wider audience. However as described by Jonas Boström at the recent Chemistry on Mobile Devices Meeting Virtual reality smartphone apps making chemistry look and feel cool. This project aims to enhance the learning experience for school chemistry lessons by providing virtual reality viewing of molecules using inexpensive Google Cardboard viewers available online.
Virtual reality smartphone apps are making chemistry look and feel cool. This project aims to enhance the learning experience for school chemistry lessons by providing virtual reality viewing of molecules using inexpensive Google Cardboard viewers.
The power of the latest generation of smart phones has enabled scientists to also explore augmented reality. Augmented reality is now being used in a number of situations. To enhance publications as demonstrated by Alistair Crow, if you want to know how to do this instructions are available here. Many people have probably used the superb ChemTube3D website created by Nick Greeves at the University of Liverpool which is an invaluable education resource, this is also accessible via a Smartphone app.
ChemTube3D contains interactive 3D animations and structures, with supporting information for some of the most important topics covered during an undergraduate chemistry degree
More recently some of the pages have been enhanced to provide access to virtual reality models, if you would like to develop similar pages there is an AppleScript droplet to batch convert Jmol files into files suitable for AR.
More recently Mark Costner has released MoleculAR: an augmented reality (AR) app to view molecules in 3D.
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
EzMol - An easy to use simple molecular graphics program
EzMol aims to fill a quite different role to that delivered by superb programs such as PyMol and Chimera. EzMol is designed at the occasional user and provides a step-by-step wizard to rapidly generate an image for inspection and publication. For example, residue selection, colouring and labelling using a paint-box approach so no typing of commands
You can read more here DOI.
A recent publication DOI describes a new application for materials science.
A new macOS software package, iRASPA, for visualisation and editing of materials is presented. iRASPA is a document-based app that manages multiple documents with each document containing a unique set of data that is stored in a file located either in the application sandbox or in iCloud drive. The latter allows collaboration on a shared document (on High Sierra). A document contains a gallery of projects that show off the main features, a CloudKit-based access to the CoRE MOF database (approximately 8000 structures), and local projects of the user. Each project contains a scene of one or more structures that can initially be read from CIF, PDB or XYZ-files, or made from scratch. Main features of iRASPA are: structure creation and editing, pictures and movies, ambient occlusion and high-dynamic range rendering, collage of structures, (transparent) adsorption surfaces, cell replicas and supercells, symmetry operations like space group and primitive cell detection, screening of structures using user-defined predicates, and GPU-computation of helium void fraction and surface areas in a matter of seconds. Leveraging the latest graphics technologies like Metal, iRASPA can render hundreds of thousands of atoms (including ambient occlusion) with stunning performance.
A recent publication DOI describes an update to the popular molecule viewer UCSF Chimera
UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution.
The application can be downloaded here http://www.rbvi.ucsf.edu/chimerax/download.html
It is important to note that ChimeraX is not backward compatible with Chimera and does not read Chimera session files. It has been tested on MacOS X 10.12. The ChimeraX user interface is implemented in Qt, offering a native-like look and feel on each platform. ChimeraX is largely implemented using Python, an interpreted programming language. To manipulate these very large datasets interactively, ChimeraX uses memory-efficient data structures combined with high-performance algorithms implemented in C++. MacroMolecular Crystallographic Interchange Format (mmCIF) is the preferred format for atomic data in ChimeraX, mmCIF replaces the aged and more limited PDB format and offers a number of advantages.
The LiteMol suite consists of three components, data delivery services (CoordinateServer and DensityServer), the BinaryCIF compression format, and a new lightweight 3D molecular viewer (LiteMol Viewer) https://www.nature.com/articles/nmeth.4499.epdf?.
You can try it out at https://www.litemol.org/.
The LiteMol suite works on all modern web browsers and mobile devices.
Among other things, LiteMol provides:
- Standard visualizations: cartoons, surface, balls and sticks, etc.
- Assemblies and symmetry mates.
- Electron Density and CryoEM maps.
- Integration with PDBe API: view and explore validation and annotation data.
- Integration with the Coordinate Server: download only parts of structures you are interested in.
- Support for the BinaryCIF format that reduces the amount of data that needs to be sent to the client several times.
A short ‘how-to’ on making macromolecular structures viewable in the ‘Augment’ augmented reality app
Allister Crow recently posted a brilliant twitter post of a movie showing a crystal structure in augmented reality: https://twitter.com/Allister_Crow/status/933000138552901632 and he posted a simple HowTo. I've taken the original instructions and expanded them to include a few extra options including how to add colours based on a comment by @tomkazimiers.
You can read the detailed instructions here.
A new production release of UCSF Chimera (version 1.12) is available: http://www.rbvi.ucsf.edu/chimera/download.html
Download is free for noncommercial use. Platforms: Windows, Mac OS X, Linux.
New since version 1.11 see release notes for the full list:
General I/O, Display:
- Updated URLs for fetching PDB, mmCIF, EDS
- improved initial display of EDS difference map (shows both positive and negative isosurfaces)
- "click-to-center" mouse mode (default Ctrl-right button) uses surface vertex instead of entire surface
- "clip" and "thickness" commands prevent placing the back plane in front of the front plane
Structure Analysis and Modeling:
- AmberTools updated to version 17
- Add Charge uses precalculated charges for NAD and NDP
- Morph Conformations "core fraction" exposed for more control over hinge detection
- "hbonds" command option to show as dashed or dotted lines
- Mol2 output includes metal-coordination bonds
- Dock Prep consistent handling of alternate locations in adjacent residues
SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems.
SAMSON has an open architecture which allows anyone to extend it - and adapt it to their needs - by downloading SAMSON Elements (modules). SAMSON Elements come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. SAMSON Elements help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more. Add new SAMSON Elements to SAMSON straight from SAMSON Connect.
In the latest news Python scripting is coming to SAMSON 0.7.0. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts. Python will make it even easier to integrate and pipeline SAMSON and SAMSON Elements with well-known packages from diverse fields, e.g. TensorFlow, PyRosetta, RDKit, ASE, etc., to name a few
Just catching up on reading the literature and came across this interesting python paper in Journal of Cheminformatics. DOI.
Scoria is useful for both analyzing molecular dynamics (MD) trajectories and molecular modeling. For example, we have used beta-version Scoria functions to create large-scale lipid-bilayer models, to construct small-molecules models with improved predicted binding affinities, to measure MD-sampled binding-pocket shapes and volumes , and to develop neural-network docking scoring functions, among other applications. As an additional example, in this manuscript we describe a trajectory-analysis Scoria script that colors the atoms of one protein chain by the frequency of their contacts with a second chain.
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
- 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
- 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)
- Changed default values for several settings:
- autoshowclassified=1 (=3 for > 500k atoms)
- “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
- 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.
SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.
This update includes
- Full integration of ReCore functionality. Now - besides fragment-replacement, joining and merging of fragments is also possible. In addition, you can fine-tune results delivered by ReCore using pharmacophore filters.
- Editing turns into full-blown designing. Besides atom by atom changes you may now add the most common rings with just one klick. So large changes can quickly be made to molecules and this in itself necessitates another new feature — namely that multiple poses are generated based on a superposition of the maximum common substructure.
- Display of torsion distribution. On the one hand, we have now integrated the latest update of the database of torsion angle distributions from the CSD, while on the other, it is now possible to view the torsion angle distribution for a particular rotatable bond.
- Miscellaneous enhancements. The SDF export covers your particular selection of favourites and any comments attached to a molecule. For a numerical filter it is now possible to define both a lower and upper bound. Last but not least, besides distances, you may now measure angles and torsions.
I've just written a review of the latest version of ChemDoodle3D
ChemDoodle 3D is a scientific visualization platform with a focus on user customizability and universal support. Just like its 2D counterpart, all of the graphics are fully customizable and controllable. The large feature set is well organized for intuitive access and we develop ChemDoodle 3D to work with the vast majority of graphics cards in use.
ChemDoodle3D really excels at the creation of high quality publication ready graphics, the ability to specifically select every atom or bond enables the user to precisely create the desired image. It performs well using modest hardware that would be accessible to any student. Perhaps one of the real attractions however is the ability to use the ChemDoodle Web Components to easily share structures via the web.
The all new SeeSAR 6 provides you with a completely redesigned and now fully customizable GUI. You can choose between different bright and dark themes and GUI layouts so that you can optimally adapt SeeSAR for different use cases.
The new design is more streamlined and customizable. Instead of having 8 different kinds of buttons in different regions of the application, we now have just a main menu top left and a toolbar top right. The main menu changes depending on the mode of use (editing, site definition, ...), while the toolbar stays the same throughout. This way you are never overwhelmed with choices, but are only presented with options that you may need. Depending on you current use case, you may also want to change the overall layout (many molecules ⇒ tables to the left; many properties ⇒ tables below to make use of the whole width; 2 monitors ⇒ tables docked out) and/or the overall appearance (bright theme for presentations; dark theme for desktop work; we have also integrated a color blindness mode just in case).
In order to give you a jump start when you begin working with SeeSAR (both as a newcomer, as well as a seasoned user of the old GUI design), we have introduced an in-application help facility in this new version. First of all, upon starting the tool for the first time or after a long break in use, SeeSAR offers you a short introductory slide show, reminding you of a few basics that can make life a lot easier. But you can also now request help from within the application with a click on the lifesaver button. The help window then shows you – context dependent – explanations on the mode in which you are currently working or on the functions that you are trying to use so you can leave the help window open, consulting it when you need it. Of course you may also navigate between help pages in the help window and from there access online resources such as tutorial videos.
There is also a free webinar: introduction to SeeSAR 6.0
It has been a little while but ChemDoodle 3D is out, and looking at the new features it was certainly worth the wait, this is a major upgrade!
New features in ChemDoodle 3D v3:
- Faster and more advanced shaders for the most realistic graphics or captivating cartoon rendering. There are now 6 shaders to choose from.
- Fully customizable and dynamic real-time shadow rendering.
- Molecules can now be built using intuitive tools and a continuous running optimization (using the new Minimizer widget) to allow you to build accurate models and the specific conformations you desire. It is a lot of fun to physically interact with the structures you build!
- New bond types, more aromatic ring representations, more cheminformatics functions.
- Distances can now be measured between any combination of bond centers and atoms; previously only atoms were allowed. Visual specifications for all shapes can now be independently edited.
- Fully customizable surfaces can now be built for selections of atoms.
- Selector tools have been added, and you can now select objects by lasso and rectangular marquee.
- Our interface engine is now fully implemented including drawing toolbars, widgets, autosaving, workspace control and more.
- Style sheets (and scene settings files) can now be created, saved and loaded.
- Quaternions can now be used for all rotations, instead of just X-Y axis rotation.
- Full support for the new RCSB MacroZZmolecular Transmission Format.
- A more advanced copy and paste system.
- After effects are new multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.
- Outlines are now rendered for highlighted and selected objects.
- Model settings in the Visuals panel in Preferences are now organized by model type.
- A new Custom Element Color Set. Color choosers have been upgraded and now affect graphics in real time. Improved MacOS look and feel.
- Added the last of the new element names recommended by IUPAC. Added more published van der Waals values.
- Polishing, new icons, and performance improvements affecting just about every asproect of the product, from picking to animations to rendering and saving images.
Chirys View is a simple molecular spreadsheet for Mac OSX. It has been designed as a fast viewer for collections of molecules represented as an SDF file (Structured Data Format). On import molecular weight, exact mass, molecular formula, hydrogen bond acceptor and donor counts are automatically calculated. You can combine multiple SDF files by multiple file imports or by coping and pasting from one document into another. You can then save selected compounds as new SDF file.
I imported 1 million structures from ChEMBL and whilst it took a few minutes to load and used 27GB RAM it did so without complaints, scrolling down a list of a million compounds is a little impractical but list sorting is pretty responsive. I had a look at some of the more complex structures and they molecular layout seems excellent and clearly legible.
As a simple molecular selection tool Chirys View works very well. My only complaint is that when you import 3D structures (e.g. from a docking run) the structures can be difficult to discern (see below), it would be nice to have a convert to 2D option.
I've only just noticed that UnityMol has been updated.
UnityMol is a molecular viewer and prototyping platform for the Unity3D game engine developed by Marc Baaden's team in Paris. It includes HyperBalls designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg). It can read Protein Data Bank (PDB) files, Cytoscape networks, OpenDX maps and Wavefront OBJ meshes.
There is a UnityMol WebGl demo available http://www.baaden.ibpc.fr/umol/webgl/ which gives you a great way to explore the display options now available.
A while back I mentioned a JMOL script for creating files for 3Dpriting the paper desiring the work has now been published in Journal of Cheminformatics DOI.
Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files.
The Jmol 3D Print website allows the creation of STL and VRML files for 3D printing for any structure in the Open Crystallography Database. You can search either the full COD and then design your own model for printing, or search the more than 30,000 predefined sample files in the figshare collection and download the STL or WRL files that have already been created for those structures.
There is more information on the 3D printing page
I just noticed that the latest version of iBabel has been downloaded over 1000 times, this is fantastic news and it certainly allows me to justify the effort put into creating the application.
I’m occasionally asked about the best way to install OpenBabel and I usually refer people to the page I wrote on installing cheminformatics tools on a Mac, this gives instructions on how to install a wide variety of cheminformatics toolkits and applications.
If you only want to install Openbabel then the best way is to use Homebrew.
Homebrew is a package manager for Mac OSX that installs packages in it’s own directory then symlinks the files to /usr/local. To install Homebrew you first need to have access to the command line tools for Xcode, the easiest way to do this is to download Xcode from the Mac Appstore
- Start Xcode on the Mac.
- Choose Preferences from the Xcode menu.
- In the General panel, click Downloads.
- On the Downloads window, choose the Components tab.
- Click the Install button next to Command Line Tools. You are asked for your Apple Developer login during the install process.
Or You can download the Xcode command line tools directly from the developer portal as a .dmg file. https://developer.apple.com/downloads/index.action. On the "Downloads for Apple Developers" list, select the Command Line Tools entry that you want.
To install Homebrew type this command in the Terminal
ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
The 'brew doctor' command checks everything is fine. e.g. it will warn if the developer tools are missing, and if there are unexpected items in /usr/local/bin and /usr/local/lib that may clash and might need to be deleted.
It is a good idea to first update the package list
To install a range of cheminformatics packages we can use a custom “tap” created by Matt
brew tap mcs07/cheminformatics
Then to specifically install Openbabel use
brew install mcs07/cheminformatics/open-babel
To check OpenBabel is working type this in a Terminal window:
obabel -:'C1=CC=CC=C1F' -ocan Fc1ccccc1 1 molecule converted
Molmil has been designed as a light-weight and full-featured viewer for the PDB. As such, Molmil can load legacy PDB flat files, PDBx/mmCIF and PDBML formatted files. Molmil can also load a custom format which we call PDBx/mmJSON, which is a JSON version of the PDBx/mmCIF data. Other formats which Molmil supports are GRO, MOL2, MDL, CCP4 (for electron density maps and EM data), MyPresto’s trajectory format, Gromacs’ TRR and XTC trajectory formats and our own developed MPBF polygon format which we are using for our eF-site service for large structures. Users can also load these files from their local hard drive.
The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.
An update to UCSF Chimera (version 1.11) is available for download.
- model-display checkboxes can be shown below the command line, and the model-active checkboxes can be hidden (see Preferences, Command Line)
- new input format: IMAGIC density map
- mouse focus (so that Chimera accepts typed input) can be restored by clicking into the Side View as well as the main window
- command-line “atomspec” expanded to handle surface piece names (such as from Multiscale Models)
- new flat ribbon publication preset
- “wall-eye stereo pair” option added to Save Image dialog
- revamped Getting Started tutorials, new Ribbon Styles image tutorial
- molecule descriptions (shown in the status line on mouseover) now read from mmCIF, not just PDB
- PubChem fetch changed to get structures from PubChem3D (NCBI) instead of Pub3D (Indiana University)
- command history navigation skips completely identical lines, and additionally pressing Shift (along with Ctrl-p, Ctrl-n, ↑, or ↓) goes to the previous/next occurrence of the same command (same initial string) instead of the * immediately adjacent command
- atom specification tolerates spaces after commas
- implemented standard keyboard shortcuts Ctrl-o,s,S,q (on Mac, Command instead of Ctrl) for File menu entries Open, Save Session, Save Session As, and Quit, respectively
This is the last release for 32-bit operating systems, both the 32-bit and 64-bit versions run on Mac OS X 10.8 or later (including OS X 10.11 "El Capitan")
Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).
I'm making increasing use of iPython notebooks and this package looks like it will be very useful.
nglview is a Python package that makes it easy to visualize molecular systems, including trajectories, directly in the Jupyter Notebook. The recent 0.4.0 release of nglview brings a convenient interface for visualizing MDAnalysis Universe and AtomGroup objects directly:
The notebook widget allows you to rotate and zoom the molecule and lets you select atoms by clicking on the molecule.
Easily installed using PIP
pip install nglview
There have been a number of comments and responses via twitter highlighting this superb demo.
The project is on Github, feel free to contribute!
The latest version of iBabel has now been downloaded over 400 times since it was released in January.
iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and molecule viewers
BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed to reduce development times in the field of Computational Molecular Biology and Molecular Modeling. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.
BALLView is BALL’s standalone molecular modelling and visualization application. Furthermore, it is also a framework for developing molecular visualization functionality.
It can be downloaded from here and requires
- CMake >= 2.8.12
- Python 2.7
- Qt 5.4
Installation instructions for Mac OSX are here
I've just added Unicon and Mona to the alphabetical listing of applications.
UNICON is a command-line tool to cope with common cheminformatics tasks. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensemble.
Mona is an interactive tool that can be used to prepare and visualize large small-molecule datasets. A set centric workflow allows to intuitively handle hundred thousands of molecules.
ChemDoodle 3D has been updated and in addition for a limited period any customer that upgrades to or purchases ChemDoodle 8 will receive a free license for ChemDoodle 3D v2.
New features in ChemDoodle 3D v2:
- Full Retina display support on Mac OS X.
- Support for high DPI Windows hardware.
- The visual specifications of the scene can now be applied to selected content, or individual objects, as opposed to the entire scene. Right-click on objects and select the Format… menu item to show visual options for that object. New representation quick buttons are now available for modifying residue atoms and bonds, ribbon models and nucleic acid models in addition to non-residue atoms and bonds.
- Protein and nucleic acid information can now be loaded from PDB files. Ribbon, trace and tube models can be generated for proteins. Ladder models can be generated for nucleic acids. The models are fully customizable. Control dimensions, alpha helix widths, coloring and more. Both B-spline and Catmull-Rom splines can be used to generate models. Water can be displayed as stars. Residue atoms can be controlled separately from hetatoms. Load PDB files by PDB id.
- Periodic data can now be loaded from CIF files. Unit cells of any geometry are resolved. Functions for periodic systems will be provided in the Periodic menu. Build supercells.
- An advanced selection system has been implemented. Select, deselect and reselect content. Select all, next molecule, inverse and by SMARTS. Use the new selection mode to select content or use the selection window to list the contents of the scene and select the content you wish to work with. The selection window is very advanced and will show you what you are currently hovering.
- Fogging can now be defined in scenes using linear, exp1 or exp2 algorithms. Fog color can be defined as well as fog ranges.
- A compass can be added on the bottom left of the scene or through the camera’s origin.
- 3D scenes can now be printed.
- Added quick quality options in the View menu to quickly switch between a range of higher and lower quality rendering settings to allow you to improve graphics or performance.
- Image export now allows for transparent backgrounds in capable image types. This allows you to easily use ChemDoodle 3D generated graphics in various media with custom backgrounds.
- Many new smaller features: added an option to remove shadows from text, added projection menu items, certified the correct 3D stereochemistry is generated from 2D drawings, picking can now handle any number of objects, and more.
- Updated to support ChemDoodle Web Components v7. Shapes can now be read/written using ChemDoodle JSON.
- Your iChemLabs account can now be accessed from ChemDoodle 3D. ChemDoodle 3D customers receive a free account for accessing ChemDoodle Mobile. If you also have ChemDoodle desktop, this is the same account.
- Dozens more improvements and additions.
iBabel started out as an AppleScript Studio application designed as a front-end to OpenBabel DOI, this was updated several times and is now an ApplescriptObjC application built with Xcode. As well as acting as a front-end to OpenBabel it also provided a front-end to tools built on OpenBabel and a molecule viewer using a selection of java applets and plugins via an embedded web view.
Now things have settled down a bit I've restarted work on iBabel and an update is now available.
I've transitioned most of the calls to babel over to obabel the differences are highlighted here and replaced the calls to the tools based built on OpenBabel with the new corresponding calls to obabel.
Lucas is a novel program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling.
Journal of Cheminformatics 2015, 7:16 [DOI](http://dx.doi.org/10.1186/s13321-015-0060-z}
The source code is available on Sourceforge
Reading through the discussion on Scientific Applications under Yosemite it seems some people are having problems with PYMOL, I thought I'd mention that installation of PYMOL using Homebrew is included on the page describing how to set up a Mac for Cheminformatics. The page also describes how to install a wide range of other useful tools.
BioBlender, the molecular visualization and animation tool based on Blender, is now an Open Program on GitHub. You can find it here: https://github.com/MonZop/BioBlender.
BioBlender is an addon for Blender, aimed at providing tools for the import and elaboration of biological molecules. It consists of several functions, some executed by Blender and/or its Game Engine, and some others performed by external programs, such as PyMOL, APBS etc.
It was developed by the Scientific Visualization Unit of the Institute of Cliniclal Physiology of the CNR of Italy in Pisa, with the contribution of several colleagues.