Molmil user manual

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Introduction

Molmil is a molecular viewer developped by PDBj and used in PDBj services same as jV. It works with typical web browsers. It can be used for embedded objects in web pages as well as for stand-alone viewer.

Usage

In Molmil, the loaded object such as molecules can be operated by a typical mouse with two buttons and a wheel.

Operation		Method
Move	Rotation around the current center	Left drag (drag with pressing the mouse left button) Swipe (with the touch interface)
	Rotate around the selected atom(s)	Ctrl + Left drag (drag with pressing the Ctrl button and the mouse left button)
	Translation to the X/Y direction (top/bottom/left/right direction of the display surface)	Translation of a loaded model can be done using one of the following methods: Shift + Left drag (drag with pressing the Shift button and the mouse left button) Left-right drag (drag with pressing the mouse left button and right button) Wheel drag (drag with pressing the mouse wheel button) Swipe with two fingers (with touch interface)
	Translation to the Z direction (before/behind direction of the display surface, zoom in/out)	Translation of a loaded model can be done using one of the following methods: Right drag (drag with pressing the mouse right button) Wheel (rotate the mouse wheel) Gesture to top/bottom direction with two fingers (move two fingers forward to top/bottom direction with keeping them touching to the trackpad and a bit space in between them) Pinch in/out (move two fingers closer/farther with keeping them touch to the touchpad/touch display)
Atom selection	Single atom	Atom selection can be done using one of the following methods: Click Tap (with touch interface)
Atom selection	Add atoms to the selection	Ctrl + click (click with pressing the Ctrl button)
Show atom information and context menu		It can be done using one of the following methods: Right click Long tap (with touch interface, keep touching the destination atom for half a second)

Selecting on the backbone in cartoon mode will select the nearest alpha carbon (CA).

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:

Supported file formats

Currently Molmil can load the following types of files. For the embedded Molmil, it usually include directions of data loading, so the users don't have to take care about it.

PDBx/mmCIF
PDBML (all-atom)
mmJSON
PDB (flat)
Polygon-XML
GRO
CCP4
MyPresto trajectory format
Gromacs trajectory format (trr/xtc)

Please note that loading files on iOS is not supported (due to the lack of a file system).
Molmil can download PDB entries and chemical component entries directly from the PDBj website simply by giving the pdbid/comp_id.
Molmil can save images as PNG images and create movies with some additional software to stitch images together and encode it into an mp4 file.

Created: 2018-10-16 (last edited: more than 1 year ago)