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Introduction

The Molmil viewer has been integrated into many of PDBj's services in a similar fashion as jV. Furthermore, Molmil can also be used as a standalone viewer.

Controls

Molmil works best when controlled with a standard mouse.

Rotation:

A loaded model can be rotated by pressing the left mouse button and then dragging the cursor along the screen in the direction of the desired rotation. When using a touch interface, swipe your finger across the screen in the desired direction.

Translation (x/y plane):

Translation of a loaded model can be done using one of the following methods:
  • Hold the shift key and the left mouse button and drag the cursor along the screen in the direction of the desired transformation
  • Hold the left and right mouse button and drag the cursor along the screen in the direction of the desired transformation
  • Hold the scroll button and drag the cursor along the screen in the direction of the desired transformation
  • When using a touch interface, place two fingers next to each other on the screen and swipe in the desired direction.

Translation (z plane, i.e. zooming)

Translation of a loaded model can be done in one of the following manners:
  • Hold the right mouse button and drag the cursor along the screen in the direction of the desired transformation
  • Scroll using the scroll button to zoom in and out
  • When using a touch interface, place two fingers next to each other with a bit of space in between (at least two fingers) and move the fingers closer together to zoom in and farther apart to zoom out.
On Macs the following method is available (when not using a standard mouse):
  • Using the mac-mouse (or touchpad) move two fingers which are about 2cm apart in the direction of the desired transformation

Picking

Click on an atom to select the atom (selecting on the backbone in cartoon mode will select the nearest C alpha). To select multiple atoms hold the Ctrl button while clicking. To rotate about an selected atom, hold the Ctrl button and the left mouse button and drag the cursor along the screen. Right clicking on an atom (or backbone) will show a context menu with some information about the atom and some styling/colouring options. On a touch screen, tap on an atom to select it. Alternatively, pressing on the screen for half a second will bring out the context menu.

File support

The integrated version of Molmil (into the PDBj web interface) will automatically load the corresponding data into the viewer. The standalone version however currently has support for the following file formats: Please note that loading files on iOS is not supported (due to the lack of a file system). Furthermore, Molmil can also download PDB entries and chemical component entries directly from the PDBj website simply by giving the pdbid/comp_id.

Molmil can also save images as PNG images and create movies with some additional software to stitch images together and encode it into an mp4 file.
2014-08-21 (last edited: more than 1 year ago)2015-12-08
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