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iMolview a Mobile App for iPhone/iPad and Android


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Explore 3D Molecules With Your Finger Tips

iMolview is an app for the iPhone/iPad and Android that lets you browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface. Touching the molecules via the screen allows you to interact immediately with the 3D structures in a unique way. You can zoom in and out, rotate, spin, pan, and clip the 3D molecules with your finger tips in ways that are impossible using a traditional mouse and desktop computer.

Download

iMolview can be downloaded directly onto your iPhone or iPad by visiting the Apple App Store. or onto your Android device Google Play Store.

Screenshot Gallery

iMolView

Fully Interactive Molecules on the iPhone and iPad

Fully interactive molecules at your finger tips!

New in v1.5 Distances and Angles

Measure and display distances and angles.

New in v1.5 Superimpose Protein Structures

Load multiple protein structures and superimpose.

Fully Interactive Molecular Documents

Read in fully interactive documents created in ICM-Browser.

Browse protein, DNA, and drug molecules in 3D on the iPhone or iPad

Browse molecules from the Protein Data Bank and DrugBank - zoom in and rotate!

Customizable Representations

A rich set of customizable molecule representations, colors and inertia rotation.

Display molecule surfaces

Download chemicals and proteins and display their molecular surfaces.

iMolview Menu Options

A rich selection of features to choose from.

Slide Menu (v1.4)

Save a representation of your 3D molecule in a fully interactive 3D slide.

Save Documents (v1.4)

Save all your slides in a single file document.


Watch iMolview in Action


Features

iMolView allows you to search for drugs such as 'ibuprofen' or 'gefitinib' in DrugBank, or proteins like 'insulin' or 'thyroid receptor' in the PDB and immediately explore their structure and annotation. This handy app allows you to quickly and easily view and interact with 3D molecules anywhere and at any time whether you are at the bench, at a conference, or just having coffee with colleagues!

The key features are:
  • Easy to use touch interface.
  • Save structure and slides (molecular document).
  • A direct link to the Protein Data Bank (PDB) and DrugBank.
  • Structure files (pdb/icb) sync with iTunes.
  • Supports retina display
  • Display and contour electron density maps
  • Superimpose multiple objects
  • Side by side stereo
  • Angle and distance measurement
  • Each molecular view can be customized with a rich set of molecular representations including: wires, balls-and-sticks, space filling, ribbon diagrams, and molecular surfaces.
  • Zoom in and out, rotate, spin, pan, and clip the 3D molecule.
  • Search and download structures from NCBI website.
  • Read in any PDB file from any URL.
  • A wide selection of coloring schemes is available.
  • Color background, color molecule by atom type, chain, N- to C- terminal, and secondary structure.
  • Select residues, atoms, or chains and color or change their representations individually.
  • Select residues in sequence and get the corresponding selection in 3D.
  • Select the whole chain by holding the corresponding tab.
  • Display fog effect.
  • Set 'inertia' to the maximum and let your molecule spin in 3D indefinitely.
  • Display residue and site labels for the whole object or selection.
  • Direct link to PubMed, Uniprot, and RCSB.
  • Read in your own MolSoft ICM *.icb files.

Release Notes

Note: iMolview is under active development and is frequently updated with new features and bug fixes.

Version 1.7

  • Added 'Tools/Load Electron Density Map' to download crystallographic data for the currtently loaded object
  • Toggle map display in 'Misc' menu tools

Version 1.6

  • Added interface to Dropbox (Documents/Dropbox)
  • Added molecular skin/surface representation
  • Added "Tools/Filter Selection" to adjust the current selection by various parameters
  • "Color Selection" can color individual representations.
  • ICM scripts embedded with the ICB file are available in the menu.
  • Added full screen mode.
  • Added interface to the ICM command language (Command tab in the search bar)
  • Tools menu (sbs stereo, measurements) appears for small molecules
  • 2D labels are displayed properly

Version 1.5

Major:

  • retina (high res) display support for the new iPad
  • multiple object support + superimpose

Others:

  • assign secondary structure
  • images in html pane
  • side-by-side stereo
  • angle and distance measurement
  • email screen shot

Version 1.4

  • added auto 'rocking&rotation mode'.
  • custom URL scheme imolview:// is extended to allow open document on the particular slide (from the webpager, keynote or other apps)
  • Added the ability to save molecular document (structure + slides).
  • Added the ability to save view and representation (slides).
  • Fixed memory leak in xstick display
  • Fixed crash in 3D labels

Version 1.3

  • support for horizontal screen orientation
  • support for custom URL scheme (imolview://)
  • search results are now scrollable and load more hits
  • VGA output on iPad and iPhone4 (3D view is mirrored, 'laser pointer' appears on touch and hold)
  • improved selection in sequence view (residue range is shown). Fixed bug with selecting single residue.
  • added atom labels display
  • added centering without zoom (via center button in menu)
  • preferences are now persistent even if the app is closed and opened again
  • added preference for hydrogen display (none/polar/all)
  • added default url preference for loading molecules off a web page

Version 1.2

  • issue with older iPhone/iPod devices FIXED
  • structure files (pdb/icb) sync via iTunes
  • download history
  • easy toggle of individual molecule display via sequence view tabs
  • faster refresh in CPK representation
  • display tools popup bar on selection
  • improved handling of very large structures
  • neighbors in other chains selection, such as atoms in the vicinity of selected ligand
  • external links menu: Uniprot and RCSB entries in addition to PubMed
  • atom type coloring for hetero-atoms only - allows combining chain-specific colors and atom type color coding
  • 3D residue picking is now tracked in sequence view
  • easy clear display button (X)
  • bug/crashes fixes

iMolview Help

How to Display PDB Files

Here are some ways to read in PDB files into iMolview:

1. Enter PDB Code in the Search Panel

The standard way to read in PDB files is to simply type in the PDB code in the search panel at the top of the screen.

2. From any Website

If your PDB file is saved on a web server (at any URL) you can download it by going to the Menu button and selecting Load File(icb/pdb) From The Web.

3. Search the NCBI Web Page and Download

Load your PDB/ICB Files via iTunes

  • Connect your iPhone or iPad to iTunes.
  • Drop your PDB or ICB file into File Sharing Area in iTunes (see image below).
  • Sync your iPad/iPhone with iTunes
  • Disconnect device and start iMolview. Go to Menu/Documents and your uploaded files will be listed there.
Click to enlarge image.

Navigation in the 3D View of the Molecule

Rotate Touch with one finger and drag it in the appropriate direction. You can also let molecule spin the by flicking the screen quickly. Adjust 'Inertia' parameter in the 'Settings' section to let the molecule spin longer or indefinitely
Zoom in/outTouch the screen with two fingers and move them apart/together.
Z-RotateTouch the screen with two fingers and twist in the appropriate direction.
PanTouch the screen with two fingers and move them in any direction.
ClippingTouch and move one finger on the right margin. Touching in the top/bottom half initiates movement of the back/from clipping plane. Two finger touch on the right margin initiates slab movement (back and front plane simultaneously).
SelectTouch and hold one finger at an atom/residue until floating label balloon appears. Tap on the balloon to select.
Cancel selectionDouble tap anywhere in the 3D view.

Entire molecules/chains can also be selected by touching and holding on the bottom tab bar. Sequence segments selections are done by touching/holding on the sequence view. Once selection is initiated, beginning/end flags appear and can be dragged to extend or shrink selected sequence segment. Selections are visually represented in 3D view as green crosses floating on selected atoms.

While the selection is active, tapping on the 'target' icon in the bottom of the view centers on selected molecules/residues/atoms. Also, display representations and coloring are applied to the selection.

Saving Slides and Documents

Slide is a combination of a view point and graphics representation. In iMolview you can create multiple slides and access them later after the document was saved.

To create a slide:

  • Setup a view and representations (color, label, etc.)
  • Go to Menu/Slides and choose "Save Current View"
  • Give a name and press 'OK'. It should appear in the list

Repeat these steps to create more slides

To modify or delete an existing slide hold your finger over the appropriate item. The possible actions are:

  • Rename: Rename the slide
  • Overwrite : overwrite the slide with the current view
  • Delete : delete the slide

To switch between slides you may use Menu/Slides or arrows on the sides of the center button.

After all slides are done you need to save your molecular document. Goto Menu/Documents/Save Current Document and give it a name. The document will be saved into History folder and can be loaded later. This file can also be copied to your PC,MAC or Linux and opened with free ICM-Browser, or you can embed this document as a live 3D object into web page using ActiveICM technology.

Displaying Electron Density

Tools/Load Electron Density Map

Loads electron density map from Uppsala EDS server (http://eds.mbc.uu.se/eds/). Once map is loaded you can toggle its display using 'Misc' panel in the main menu. In addition map can be contoured around selected atoms:

  • Select part of the molecule
  • Click on the contour icon in the 'Misc' panel on the pain menu.
  • Contouring level can be adjust using slider in the 'Tools' menu.

New icons in 'Misc' panel:

  • Map view toggle: [Optional] toggles display of the electron density map (if loaded). (See Tools sections to see how to load a map)
  • Map Contour toggle: [Optional] Contour density map around selected atoms. Contouring level can be adjusted in the Tools menu.

Using custom URL scheme imolview://

Custom URL scheme can be used to launch iMolview from different applications (Safari, Keynote and others). It has the following format:

imolview://[][?PARAM=VALUE&PARAM=VALUE]

  • PATH_TO_THE_FILE can be either relative local path to the Documents folder. (History/3gvu.icb) or absolute URL (http://side.com/folder/file.icb)

    Supported file types are:

    • ICB: Molsoft molecular document format. May contains multiple molecular objects, meshes slides and others.
    • PDB: Protein Data Bank file.
    • MOL/MOL2: MDL or Tripos small molecule file.

  • PARAM can be one the following:
    • BGCOLOR: redefine the background color. The VALUE should be a color name.
    • PDBCODE: loads PDB structure with the code from VALUE. If you have this field PATH_TO_THE_FILE should be omitted.
    • SLIDE: sets the slide. The VALUE should be either slide name or number
    • RUN: runs a list of semicolon (or new line) separated lits of ICM script commands.

Examples:

# opens the document and sets the default view.
imolview://History/3gvu.icb
# opens slide 1
imolview://History/3gvu.icb?SLIDE=1
# opens slide 'Slide2'
imolview://History/3gvu.icb?SLIDE=Slide2
# opens default view for PDB '1xbb' sets background color to white
imolview://?PDBCODE=1xbb&BGCOLOR=white
# loads PDB and highlights the ligand
imolview://?PDBCODE=1xbb&BGCOLOR=white&RUN=display a_A,N ribbon transparent;color 
ribbon rgb={200,200,200}; display cpk xstick a_H; center a_H

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