NDKmol - molecular viewer
- Molecular Viewer for Android
== 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 inWebGL/Javascript and runs on Web browsers. You can try GLmol at http://webglmol.sourceforge.jp/index-en.html
== Features ==
* Read PDB or SDF/MOL file
* Rotate/Translate/Zoom model by finger
* Representations
- Line
- Stick
- Sphere(van der Waals radius)
- Alpha carbon trace
- Ribbon (Thin or Thick)
- Strand
- B factor tube
- Nucleic acid ladder
- Nucleic acid line
- solvent 'stars'
* Smoothing of beta-sheets
* Coloring
- By chain
- By secondary structure(when defined in SHEET/HELIX records)
- By Elements
- Gradation (a.k.a chainbow)
- B factor
- polar/nonpolar
* Crystallography
- 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 protected]
=== LICENSE notice ===
NDKmol itself is licensed under GNU Lesser General Public License as follows.
However, PDB files included as examples are under DIFFERENT conditions.Please consult http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/pdb_advisory.html
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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 .
Category : Education
Reviews (29)
This is the best application i have ever installed. i love it how they managed app size + 3d view + additional view settings in simplest way. good job guys.
Only works with some phone models. Needs a so-called menu button which Samsung phones lack. App is useless on my S6.
Updated android (10.1) menu gone:( any fix?
I really liked this app and it was really useful to me even during my Mres project. But once I switched to a new phone (Sony Xperia XZ Premium), I cannot use this app anymore. Every time I try to download a structure, it gives me an "error occured while downloading a structure". I hope there is a fix for that.
Android needed a pdb viewer and this one is far better than I ever would have expected. Props to you Dev! There are some minor things (would love an option drawer instead of the option circle and some metal ions wouldn't show up) but very nice overall
Who would have thought we could have such smooth and precise graphical imagery on our pockets, for free? The loading tray/library could use some.work, but I can't ask much more from such an awesomely entertaining app.
Wonderful idea for introducing this app.I am speechless to say anything.Who so ever that "mind" is seriously true intellect:)
The only suggestion would be ability to long press a residue and get name/#.
I can't download anything from PDB. It always says some error has occurred. Please help !
The provided molecule is great, but every time I try to download another, I am told there is an error. I therefore seem to be stuck with just one molecule...is there a way to fix this?
Excellent quality, easy to use. For a new release, it would be nice to be able to select the different residues.
This app is so great. It allows extensive molecular visualizations with the limited power of a handheld.
Just wish i could view aa sequence
Can't work on Android 7.
Can't search at all! What's up with this? If Icould search it would be the best app
CAN'TT OPEN THE MENU
Only one molecule
I recently purchased a Note 10.1 2014, and I was curious if there were any android apps that would let me fetch and view protein structures from the PDB. This app far exceeded my expectations. It has the smoothest rendering of any viewer I've used, including desktop applications. It allows various color options, display of the biological unit, fetching from the PDB. I'm sure there are some advanced options that were removed, but for a tablet viewer, I'm hugely impressed.
Renders really fast, looks gorgeous, and gives good display options with an unobtrusive interface. Can display the PDB header. However, I have an ASUS Transformer with a dock, so I need to keep my tablet oriented landscape. NDKmol's inability to handle landscape orientation lost it 2 stars (again, I NEED it landscape). Also, I would like to see what individual residues are, as well as ligands--perhaps with one tap.
Well done. It would be nice if you add some sort of sequence instrument like s button in pymol.
Worked fine till I upgraded to lollypop. Now it opens and appears to download molecules but does not display them.
Great work. The only thing required is to allow the nucleic acid structures to render as well. Which makes it better
Does not open on my Samsung Tab S, worked with EsMol, for those who do not have a menu button I got this to work with the menu button on my Samsung keyboard, would be much more useful if amino acid sequences could be displayed like in Pymol
Extremely well built, just one thing though. Add drawing and SMILES capabilities plz.
Used to love this all, but it stopped working after upgrade to Lollypop (Nexus4)
I love that NDKmol recognises ligands and draws them in a different representation to the protein. The feature I would like to see most now is trajectories (e.g. when frames in a PDB are separated by END cards). More multi-touch support would also be nice: 2 finger drag to move (similar to how you change pitch in google earth), and 2finger rotate to allow rotations in the axis perpendicular to the screen. I can see myself using this app in meetings with my supervisor.
When I open the app I only see what I think is the initial splash screen molecule? No menu is visible or accessible from any point on the screen. The molecule looks wonderful and is fully interactive and easily controlled which makes me very sad that I can't use this app.
This app is fantastic. Smooth and renders beautifully. Would love it if you could include stereo views as well.
How come there is no answer from the developer on the menu issue? I cannot just open up an on-screen keyboard to access a menu function as someone suggested for their tablet. How foolish to make this app without a menu in it!