The SIB Swiss Institute of Bioinformatics presents:
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v4.1
by Nicolas Guex , Alexandre Diemand , Manuel C. Peitsch , & Torsten Schwede
Freestyler Magic 3d Easy View Missing Arm
- Please note that Swiss-PdbViewer is a 32 bits application and will * NOT * run on OSX Catalina
If you absolutely need it, refrain from updating, boot from an older OSX version, or use the PC version within a virutal machine.I currently have no plan to update it to run on OSX 10.15 - For information, v4.1.1 works up to OSX Mojave (10.14).
Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
Swiss-PdbViewer (aka DeepView) has been developped since 1994 by Nicolas Guex. Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.
Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.
Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and residues can be mutated.
Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. An example can be found here.
- The major change compared to 4.04 is the abandon of the default non openGL rendering mode which was causing various color issues on recent Apple hardware.
- New tool: Possibility to detect hydrophobic patches, see tutorial
- New tool: Detection of grooves (open cavities)
- New tool: Detection of contact surfaces, see tutorial
- Added an atom radius table in the usrstuff directory. This can be modified to override the default size of the spheres drawn on screen for a given atom type.
- The blast against Uniprot feature has been fixed
- Improved the readibility of the Motif search feature.
- The URLs to import uniprot entries have been updated
- Fixed the Select AAkind submenu issues on the PC version
- The Thymine C6 atom is now correctly loaded
- Fixed the POV-Ray output endless loop on the PC version
- The occasional crash while saving PDB files (such as 2i37) on the PC has been fixed
- Updated the address of the Uppsala Electron Density Map Server
- First of all, and most importantly, PC and Mac versions have been resynchronized.
- Support for direct login modelling submissions and result retrieval to/from the SwissModel Workspace
- Enhanced Import Menu
- Enhanced user interface with taxonomy support, and new sequence alignment features.
- Beta version of 3D Motif Searching feature
- Easy access to external user defined scripts directly from the interface
- Revised Help files accessible from the interface
If you have FreeStyler already installed, skip to the Magic 3D Easy View installation section.
FreeStyler Installation
- FreeStyler requires Microsoft Net 3.5 to run. If you do not have Windows 10 or later, download and install it from https://www.microsoft.com/en-ca/download/details.aspx?id=21
- Download and install FreeStyler from http://users.telenet.be/freestylerdmx/
- IMPORTANT: By default, FreeStyler installs into the C: drive's root directory “C:FreeStyler”. A better directory to install into is “C:Program Files (x86)FreeStyler” folder. This is the “proper” installation folder for Windows programs. The term directory (DOS command prompt term) and folder (Windows desktop term) indicate the same thing.
- A Windows Firewall window will pop up during the initial install. You want to give permission for Freestyler to access the network. I allowed all 3 options which may not be necessary.
- During the install, check the checkbox to download and install Magic 3D Easy View. It is really just a “download” option. It will install Magic 3D before installing the rest of Freestyler.
If you missed selecting the checkbox, all is not lost! Go to Nicolaudie and download the latest version.
Magic 3d Easy View Installation
If you did not check the checkbox to install Magic 3D.
- IMPORTANT: Install Magic 3D Easy View into the SAME folder as where FreeStyler was installed in. The default location for FreeStyler is “C:FreeStyler”. If you followed this guide for installing both FreeStyler and Magic 3D Easy View then use “C:Program Files (x86)FreeStyler”. If not, use the directory where you installed FreeStyler,most likely the default location “C:FreeStyler”.
- A Windows Firewall window will pop up during the initial install, I allowed all 3 options which may not be necessary.
- During Magic 3D Easy View installation, it will also install the SIUDI Drivers into the C:SiudiDriver root directory. These are used if you have a Sunlite USB to DMX controller.
Testing
You will open Magic 3D Easy View from within FreeStyler. This allows FreeStyler to control Magic 3D Easy View. Normally, you will not run Magic 3D Easy View on its own.
- Select the Virtual Interface. If it doesn't automatically open to selecting the interface, go to FreeStyler Setup and select Interface Setup.
- You should also see the 3D icon enabled in FreeStyler menubar. This indicates that you've installed Magic 3D Easy View into the same directory as FreeStyler. If the icon is greyed out, then reinstall Magic 3D Easy View into the FreeStyler directory.
- After clicking on the 3D icon, the Universe Patch dialogue window will open. There should be the option for the FreeStyler DMX Universe shown. If not, then go back and check your installation of Magic 3D Easy View.
- Once the Magic 3D Easy View window opens, you should see:
Important Checks:
- Indicates that it is “Controlled by FreeStyler”
- Indicates that it is in “Eco Mode” and not “Demo Mode”. Demo Mode is used when no virtual or hardware DMX interfaces are found.
Freestyler Magic 3d Easy View Missing
If you've gotten this far, then it is working and good to go.
Problem/Glitch:
When I first turn on my computer and run FreeStyler then hit the Magic 3D Easy View button, sometimes nothing happens. Exiting FreeStyler and running it again fixes the problem and then Magic 3D Easy View works.