Biomolecular visualization software settings for glasses free 3D laptop

Autostereoscopic laptop prerequisites
In order to enable the 3D molecular visualization software, the following tools need to be installed on Windows 7 operating systems.
1.Qosmio F750 (3D model) Win7 64bit: nVidia Display Driver update Version 8.17.12.9039
2.Qosmio F750 (3D model) Win7 64bit: Super-D IC Driver update version 1.0.1613.809
3.Qosmio F750 (3D model) Win7 64bit: Toshiba® Blu-ray Disc Player 1.0.0.871
4.Qosmio F750 (3D model) Win7 64bit: Toshiba® Blu-ray Disc Player update version 1.0.1.299_A
5.BIOS version 2.00 upgrade for Qosmio F750 (for PQF70*, PQF75*)
6.Super-D X-tune for Qosmio F750
Items 1 to 6 can be downloaded from Toshiba®’s supporting website .
7.3D Screen Activator developed by Kevin Cox is required to enable switching between different screens.

PyMOL settings:
Install PyMOL. We have tested autostereoscopic capability on PyMOL 1.3 r1 (academic version). PyMOL allows the 3D interleaved stereo mode, which can be triggered through Zalman® stereo buttons included in the PyMOL version 1.3 packages. The Zalman® button needs to be activated outside the main program. After starting the program PyMOL and opening the associated file, go to the Menu bar and click on Display and then select Stereo. The picture is now available in interleaved format. Then, point the cursor to the right corner of the monitor, which has the ‘3D Screen Activator’ icon, choose the tab which is related to the PyMOL graphical window and then click on the 3D-interleaved switch.

3D Screen Activator

3D Screen Activator Setting for PyMOL with applicable margin width.

CCP4mg settings
Install CCP4mg-2.5.3. Start the CCP4mg program, select the Open menu item from the File menu and select a pdb file. Once the file is loaded, go to the menu bar, select the Zalman® Stereo menu item under the Display menu to activate the Zalman® stereo mode. Then click on the 3D icon from the 3D Screen Activator and select the 3D interleaved mode from the CCP4mg graphical windows to turn on the 3D display for the CCP4mg program.

Chimera Settings
Install Chimera-1.6.1. Start the program Chimera and open the file. After that, the Chimera stereo mode can be viewed from the Viewing Controls menu item under the Tools menu, Camera. A small window will appear. Choose the mode row stereo, right eye odd and then click save. After this stereo mode is activated, click on the 3D icon from the 3D Screen Activator. Select the Chimera Graphical windows and switch on the 3D interleaved mode.

Coot settings
Install WinCoot-0.6.2. Coot allows for working on the 3D interleaved stereo mode, which can be executed through the Zalman® stereo buttons. After WinCoot is started, go to the Open Coordinates menu item under the File menu, and then go to the Open Map menu item. Once the picture of the coordinates and the map are opened, go back to the Menu and then select the Stereo menu item under Draw menu. This will open the small window offering to display View Mode, and the radio button to activate Zalman® stereo. After the Zalman® stereo mode was activated, click on the 3D icon from the 3D Screen Activator. Select the WinCoot (coot_real.exe) graphical windows and choose the 3D interleaved mode. The coordinates and the map should become 3D and you are settled for 3D exploration of your favorite model.

Source: Tanramluk D, Akavipat R, Charoensawan V, Toward mobile 3D visualization for structural biologists. Mol. BioSyst., 2013, 9 (12), 2956 – 2960.

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About nanonan

Bioinformaticist and Structural Biologist
This entry was posted in 3D visualisation, CCP4mg, Chimera, Coot, PyMOL. Bookmark the permalink.

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