NDKmol - molecular viewer
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About NDKmol - molecular viewer
NDKmol -- 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 in
WebGL/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 biochem_fan@users.sourceforge.jp
=== 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
-------------
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 .
== 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
WebGL/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 biochem_fan@users.sourceforge.jp
=== 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
-------------
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 .
All Application Badges
Free
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Android
2.2+
2.2+
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Android app
App History & Updates
What's Changed
Version 0.95 (20150503)
* Fixed "Search PubChem" to work with recent server update
* Hopefully this version should work on Android 5. (Tested in Android 5.1 on Nexus 7)
If not, please send me details.
* Can open MRC map files (BETA)
To users of devices without MENU button:
there should be a way to open MENU, for example, pressing
HOME button long. Please consult the manual of your device.
Version 0.95 (20150503)
* Fixed "Search PubChem" to work with recent server update
* Hopefully this version should work on Android 5. (Tested in Android 5.1 on Nexus 7)
If not, please send me details.
* Can open MRC map files (BETA)
To users of devices without MENU button:
there should be a way to open MENU, for example, pressing
HOME button long. Please consult the manual of your device.
Version update NDKmol - molecular viewer was updated to version 0.95
More downloads NDKmol - molecular viewer reached 10 000 - 50 000 downloads
More downloads NDKmol - molecular viewer reached 10 000 - 50 000 downloads
Version update NDKmol - molecular viewer was updated to version 0.92
What are users saying about NDKmol - molecular viewer
R
by R####:
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PubChem not working
R
by R####:
by R####:
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.
R
by R####:
by R####:
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
D
by D####:
by D####:
Its interesting, but not very usable. The UI is strangely hidden, and any molecule I try to download from the PubChem just gives me an error and tells me there is no 3D view of the molecule available. It would be nice if you could filter out the incompatible molecules during searches.
M
by M####:
by M####:
Can't search at all! What's up with this? If Icould search it would be the best app
R
by R####:
by R####:
The only suggestion would be ability to long press a residue and get name/#.
R
by R####:
by R####:
Just wish i could view aa sequence
R
by R####:
by R####:
Wonderful idea for introducing this app.I am speechless to say anything.Who so ever that "mind" is seriously true intellect:)
R
by R####:
by R####:
Excellent quality, easy to use. For a new release, it would be nice to be able to select the different residues.
I
by I####:
by I####:
Only one molecule
R
by R####:
by R####:
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
M
by M####:
by M####:
Used to love this all, but it stopped working after upgrade to Lollypop (Nexus4)
P
by P####:
by P####:
Worked fine till I upgraded to lollypop. Now it opens and appears to download molecules but does not display them.
N
by N####:
by N####:
Nice
C
by C####:
by C####:
Best pdb viewer yet! Actually allows to visualize proteins as ribbons and highlights secondary structure and ligands. Loving it :)
N
by N####:
by N####:
This is a great app for checking out structures on the go, whilst reading papers on the train for example. Really impressed with the quality of the rendering. Would be nice to see space fill, and surface options.
N
by N####:
by N####:
Thanks for a great first release. Looking forward to future updates.
Y
by Y####:
by Y####:
very good start. ocationally freezes though.
N
by N####:
by N####:
Awesome... Easy to understand, easy to study . Really a good app.
N
by N####:
by N####:
Runs great, but coloring does not seem to work, ribbon structures always displayed as white.
B
by B####:
by B####:
the image is worsethan anything I have seen and you cannot manipulate the molecule as you should.
X
by X####:
by X####:
This app is so great. It does pretty extensive molecular visualizations with the limited power of a handheld. Must-see! The only missing feature is app2SD
N
by N####:
by N####:
Excellent free app to view pdbs
W
by W####:
by W####:
Works better than others
D
by D####:
by D####:
great
P
by P####:
by P####:
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.
Z
by Z####:
by Z####:
Great work. The only thing required is to allow the nucleic acid structures to render as well. Which makes it better
Z
by Z####:
by Z####:
Extremely well built, just one thing though. Add drawing and SMILES capabilities plz.
C
by C####:
by C####:
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.
R
by R####:
by R####:
excellent !
O
by O####:
by O####:
Well done. It would be nice if you add some sort of sequence instrument like s button in pymol.
E
by E####:
by E####:
Love it, helps so much in undergrad biochemistry class.
S
by S####:
by S####:
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.
L
by L####:
by L####:
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.
N
by N####:
by N####:
This app is fantastic. Smooth and renders beautifully. Would love it if you could include stereo views as well.
R
by R####:
by R####:
Was waiting for pymol to come to android, but this looks just as great, and the touch features make navigation very intuitive. The thick ribbons work just fine on my Galaxy S II and Transformer Infinity. Please make an optimized tablet version, I'd also love to be able to search and center on specific residues and active sites. I wonder how much trouble it would be to add a ray trace rendering function? ;)
R
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by R####:
Its too good.. Thanks.. Please add stereo feature too..
J
by J####:
by J####:
I guess my problem stems from not knowing how to use it, or the program not being designed for what I need. I need to view .mol files - for Phthalocyanines, Porphyrins, POMs, etc. I want it that even if my computer is screwed up, I can function and look at a molecule... help?
R
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by R####:
This app is so fluid and responsive and loaded with lots of cool features that i could not resist myself from giving it 5 stars
by R####:
How to make surface of polymer.