Do you want to see different molecules such as adrenaline, cocaine, amino acids and etc. with real 3D stereoscopic mode?
With "Molecule 3D" you can look at them with several 3D stereoscopic modes: Anaglyth, Side by Side and Mirror separated.
"Molecule 3D" helps you to understand space structure of complex molecules.
For Anaglyph stereoscopic mode you must have Anaglyph stereo glasses having red/green-blue color division.
Some people can see stereoscopic image without special glasses using Side by Side or Mirror separated mode.
You can simply open any file in PDB(protein Data Bank) format or choose some molecules in the available list and interact with it by simple standard touch control.
File browser shows files only with *.pdb, *.ent, *.txt extensions and only not empty directories.
Some basic control features:
- main menu is called by clicking on the title of the main window(where molecule is displayed) or by context menu;
- grouping, search are available by context menu in the "Molecule List" window.
Interleaved stereoscopic mode for HTC Evo 3D mobile phone is supported. It is automatically detected and added in stereo mode list.
Users of the Jmol Molecular Visualization Activity can download and investigate on their Android tablet over 60,000 biomolecular structures directly from the Protein Data Bank (PDB) by keyword or PDB ID and over 40,000,000 unique structures from the National Institutes of Health National Cancer Institute (NIH/NCI) using a wide variety of chemical identifiers, including CAS registry numbers, InChI keys, trade names, common names, and IUPAC-format names, among others. (For a full list, see http://cactus.nci.nih.gov/chemical/structure.) Files from any other internet-available site that can be read by Jmol may also be loaded.
The Jmol Molecular Visualization Activity is a nearly full touch-screen implementation of Jmol allowing for command-line entry of Jmol commands (see http://chemapps.stolaf.edu/jmol/docs) as well as a variety of preset simple visualization modes. Additional renderings include a full range of visualizations for crystals (unit cells, symmetry operators, Miller planes, for example), a wide variety of surfaces including Van der Waals surfaces, solvent-accessible surfaces, cavities, and molecular surfaces, and atomic and molecular orbitals.
Special features of the Android version of Jmol include a connection to the gyroscope, allowing for initiating of spinning by simply moving the tablet in a natural fashion (see http://www.youtube.com/watch?v=JPwvCmD5IDg and http://www.youtube.com/watch?v=D7uOkhoJ0Oc).
This activity is under active development. Feedback is much appreciated.
As moléculas apresentadas podem ser manipuladas pelos usuários, permitindo a visualização por diferentes ângulos, assim como ampliar ou reduzir as estruturas, para que seja dado destaque em áreas de interesse. Cada molécula possui um texto explicativo.
Apoio: Sociedade Brasileria de Química (SBQ), INCT Energia e Ambiente e INCT Inomat
== About ==
NDKmol is a molecular viewer for Android. You can view three dimensional structures of proteins, nucleic acids and small molecules. NDKmol supports most of common representations for molecules, such as ribbon, trace, stick, sphere and line. NDKmol also supports symmetry operations; biological assemblies and crystal packing can be displayed. You can search and download structures from RCSB PDB and NCBI Pubchem.
NDKmol has almost same functionality as GLmol, which is written in
== Features ==
* Read PDB or SDF/MOL file
* Rotate/Translate/Zoom model by finger
- Sphere(van der Waals radius)
- Alpha carbon trace
- Ribbon (Thin or Thick)
- B factor tube
- Nucleic acid ladder
- Nucleic acid line
- solvent 'stars'
* Smoothing of beta-sheets
- By chain
- By secondary structure(when defined in SHEET/HELIX records)
- By Elements
- Gradation (a.k.a chainbow)
- B factor
- Display unit cell
- Show crystal packing (when defined in REMARK section)
- Display biological assembly (when defined in REMARK section)
== How to Use ==
When launched, NDKmol automatically loads Porin (PDBID: 2POR) as an example. You can rotate the molecule by your finger.
To zoom or translate the molecule, press MENU button in your phone/tablet and select the mode. Two-finger gestures are also supported.
Everything else can be done from the MENU.
To load other PDB files, please put the file in "PDB" directory of the SD card and select "Open" command in the MENU. You can also download structures directly from RCSB PDB and NCBI PubChem web server. Select "Search and Download" in the menu.
== Contact ==
Project website is located at http://webglmol.sourceforge.jp/ . You can get source codes for this program from here.
Comments and suggestions are welcome at http://sourceforge.jp/projects/webglmol/forums/ or email@example.com
=== LICENSE notice ===
NDKmol itself is licensed under GNU Lesser General Public License as follows.
However, PDB files included as examples are under DIFFERENT conditions.
NDKmol - Molecular Viewer for Android
(C) Copyright 2011, biochem_fan
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
The trajectories of the particles are determined numerically. The well known Velocity Verlet integration of Newton's equation of motions is used for a system of interacting particles. Forces between particles are defined analytically using a "pair potential function" that depends on the distance between two particles.
In physics, MMD is used to examine the dynamics of atomic-level phenomena that cannot be observed directly. Within the mobile devices context, it can be used as a small mobile laboratory to understand the basics of the particle physics. Furthermore it can be used to produce nice dynamical pictures that are suitable as a live wallpaper.
- The application can be set as a live wallpaper that visualizes the current experimental set up.
- In the live wallpaper mode, the active “static” wallpaper can be used as a background. You can mix your favorite background picture with particles “flying” in front of it.
- The changes made in main application will be applied to live wallpaper daemon to make the wallpaper tuning easier.
- Generation of an initial structure of the particles use diagonal or square grids with given dimension
- Possibility to select a boundary condition (full energy is constant, kinetic energy is constant, or no constraints)
- If kinetic energy is constrained, it is possible to apply “thermal change” that simulates heating/cooling of the system
- Possibility to change the gravity value. The gravity vector can be also changed by rotating of the device.
- Possibility to select and visualize selected potential. Currently, three common potentials are available: Lennard-Jones, Morse and Born-Mayer.
- The particle skin can be selected from build-in clip art.
- Multi-touch interface is used to zoom and drag the experimental area.
Note: since the application implements a numerical integration method, it generates a significant CPU load. Therefore, the live wallpaper mode is not suitable for low-power devices.
Keywords: live wallpaper, HD wallpaper, physics, molecular dynamics, atom simulations, experiment
This application displays and allows you to interact (using the touchscreen to rotate) with a 3D molecular model of your choice.
You can choose a 3D model of the available molecules and interact with it by hitting the screen.
Furthermore, for each molecular model, there is information about it, you can consult.
If you want to watch a 3D model of molecules such as O2, N2, Ozone ... Do not waste time and try it!
This app provides a visual approach to organic chemistry. It is not meant to replace a textbook - it should be seen as a visual aid. The molecules and reactions are just briefly described. The main focus are the numerous animations of the molecules and reactions. Currently only alkanes, alkenes and alkynes are described. You can test your knowledge through a quiz of 40 questions.
IMPORTANT: Hardware requirements - SCREEN SIZE > 3.7 inches and DUAL-CORE CPU!
The animations are strongly compressed in order to keep the app size small. This is why the animations only run on newer smartphones!
With time I hope to add more features, easier layout.
If you have any advice or concerns please email me. Also if you have any moleculare shapes you want added please email me and I'll update it with them included.
Also this app can be transformed to be centered on other subjects. Please feel free to email me and request another version for a different topic.
NOTE: ChemDoodle® Mobile is accessed with your ChemDoodle account that is provided to you for free when you purchase ChemDoodle desktop. You can use the Guest account to access this app without purchasing ChemDoodle, but you will not be able to save your drawings and some features may be restricted.
Full 3D graphics requires Android 5+, Lollipop.
Logging into your account enables the following:
1. IUPAC naming
2. Full 3D graphics (orthographic lines otherwise)
3. 1H NMR Spectra
4. Saving structures
Thank you for all the positive feedback! Please rate ChemDoodle Mobile 5 stars so we can continue to provide you with new and free features.
ChemDoodle Mobile is the Android companion to the popular chemical publishing desktop application, ChemDoodle. ChemDoodle Mobile is a calculator for drawn organic structures. There are five main windows: Draw, 3D, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The 3D window allows you to view the drawn molecule in 3D. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive. The Help page contains a thorough help guide.
Please note that in the Android version, pinch gestures only work on platforms supporting Chrome for Android. Performance may vary depending on the Android device this app is run on. Recommended screen size of 320x480 pixels or greater.
1. IUPAC Name
2. Molecular Formula
3. Empirical Formula
4. Molecular Mass
5. Monoisotopic Mass
6. Degree of Unsaturation
7. Hydrogen Bond Acceptors
8. Hydrogen Bond Donors
9. Rotatable Bonds
10. Total Number of Electrons
11. Average Molecular Polarizability
12. Molar Refractivity
13. Polar Surface Area
14. van der Waals Volume
1. Mass Parent Peak (Isotopic Distribution)
2. 1H NMR
3. 13C NMR
In Atomify you are in charge of the universe. You are God. You can control the temperature and size of your system to see how this affects the behavior of the atoms.
Six different systems are available for study: crystal, diffusion, chamber, fracture, wall crash and bullets.
The simulation is performed with a high performance molecular dynamics model with the Lennard-Jones potential using standard parameters for argon.
Developed by Anders Hafreager and Svenn-Arne Dragly (PhD candidates at the University of Oslo).
Source code is available from https://github.com/computationalphysics/molecules (GPL v3).
iMolview lets you browse and view in 3D protein and DNA structures from Protein Data Bank, drug molecules from DrugBank, and small molecules from Pubchem. Search for drug names like 'ibuprofen' or 'gefitinib' in DrugBank, or proteins like 'insulin' or 'thyroid receptor' or pdb code in PDB. Information associated with each molecule in these databases is also at your fingertips. Sync and view your own structure files via iMolview folder on your sdcard. Molecular view can be customized with a rich set of molecular representations (wires, balls-and-sticks, space filling, ribbon diagrams, molecular surfaces) and various coloring schemes. Select residues, atoms or chains and color or change their representations individually. Set 'inertia' to the maximum and let your molecule spin in 3D indefinitely.
Please write to support[at]molsoft.com with any problems so we can follow up with technical details.
IMPORTANT! The current version has a problem with certain old HTC phones. This issue will be fixed in the next version.
Students hear the name of an organic molecule or fact spoken and choose the matching photo. They then hear more information which they will need to answer subsequent questions. After six right in a row, Race Mode starts automatically. It asks questions at speed to test the students' memory and comprehension of the molecules and facts just covered, before continuing with new molecules and facts. At the end of the race, students can see how well they have done relative to their other races. The game gradually focuses on any molecules and facts that the students have difficulty recognizing, and speeds up as competence is gained.
By contrast to Race Mode, Story Mode slowly introduces new organic molecules by saying them as the photos are shown, allowing students to quietly look, listen and learn.
The game is controlled by on-screen gestures which are simple to demonstrate and easy to use, and the game can be played without voice prompts.
* 34 diagrams of 34 organic molecules
* Rotations and reflections of each molecule
* Spoken facts
* Race Mode tests memory and comprehension against the clock
* Story Mode allows students to look, listen and learn
* Slideshow Mode displays all the molecules and facts in alphabetical order
* Zoom and Pan Mode magnifies the images to see more detail
* Easy on-screen gestures to control the game
* Context-sensitive help
The paid version of this app has much higher resolution photos than the free version. The free version has lower resolution photos and does contain advertising but no push advertising. No internet connection is required.
- Initiate nearly 300 virtual chemical reactions by dragging elements into the Reaction Area.
- Amazing images and videos illustrate the molecules you create.
- Select alternate views of the Periodic Table to discover different aspects of the elements’ chemical properties.
- Touch any of the Periodic Table's 118 elements to see an image and fun fact about it.
- With helpful hints about reactions to try, there’s always something exciting to explore.
- “Featured Reactions” menus guide you through themed sets of chemical reactions related to particular applications,such as the environment, beauty products or cars.
- Learn more about how the Periodic Table is organized, and follow links to additional educational resources.
How to use the app :
Card 1 :Find out what this molecule is and write one sentence about the molecule's geometry ?
Card 2 to 6 : Try to explain the following molecule's geometry. (hint : use Lewis, electrons pairs, lone pairs...)
Card 7 to 11 : answers for cards 2 to 6, showing molecule's geometry, electrons pair and lone pairs.
Card 12 : final answer for cards 1, molecule showing molecule's geometry, electrons pair and lone pairs.
Once downloaded this one does not require an Internet connection.
You don't have to calculate the enormous amounts of sums of a's, b's and their deltas anymore because your Android will do it for you!
We also have an iOS version! http://itunes.apple.com/us/app/id439562046