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ProteinScope connects to the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) to retrieve structure information. Advisory for the Use of the PDB Archive

ProteinScope for Mac performs limited parsing of PDB XML (PDBML) format files only. PDBML is the canonical XML format for the PDB data, and every protein on the RCSB is available in this format. Legacy .PDB file format is not supported.



PDB XML files stored on local drives will have the extension .XML with the 4 digit PDB ID as the filename, eg 9ins.xml - from the ProteinScope File menu select Open PDB From Disk... and a File Open dialog limited to .xml extension files will open for file selection. Double click the file to open, and parsing will commence. Larger PDB structures will take longer to process.

      

PDB XML can also be downloaded direclty from the RCSB PDB from the ProteinScope File menu; select Open PDB From RCSB... and a PDB ID dialog will appear. Type in the PDB ID of the structure to examine, eg 9ins, and the XML file will be downloaded from the RCSB PDB FTP Archive over HTTP. This downloaded file will be accessable via ProteinScope File menu Open Recent. The downloaded file is then parsed as described above.

      

Once the PDB file has been fully parsed, rendering setup begins. ProteinScope for Mac uses the latest Metal 2 rendering engine, exclusively on OS X Mojave. ProteinScope no longer uses the Apple deprecated OpenGL system, but larger files of many atoms may still take some time for initial scene setup and frame rendering. For this version, rendering display has been limited to 65,000 atoms per molecule - most of the Protein Data Bank deposited structures are less than 19,000 atoms.



The protein being displayed will auto rotate. Use the mouse wheel (or equivalent) to zoom in and out. ProteinScope supports full screen mode, either through the View menu option or using the current window green maximize button





ProteinScope can have multiple protein windows open simultaneously. The Window menu can be used to toggle between views.



Proteins can be displayed in different styles, Spacefill and Carbon Backbone. Atom coordinates are interpreted as 1 Angstrom = 1 SceneKit Unit. For Spacefill, the calculated atomic radius is modified for visual effect.



For Carbon Backbone, carbon alphas in the same chain are joined together in a continuous linkage



Each link between carbon alphas is colored by the residue it represents, only residue color mode is available in this display style.



The color schemes available in ProteinScope for Mac are:

Residue - based on the Shapely color scheme
Atom - based on the CPK color scheme
Chain - a unique color for each chain the residue is on
SETOR - based on SETOR: hardware-lighted three-dimensional solid model representations of macromolecules. J Mol Graph. 1993, 11, 134-138.
Temperature - Red is hotter, blue colder. Not all PDBs have this information
Hydrophobicity - Blue is more hydrophilic, red more hydrophopic





The 3D printing features of ProteinScope can accessed from the "3D Printing" top level menu.
With a protein open, 'Generate 3D Print...' will take you to the 3D print ordering sequence that is also available from the main toolbar button item 'Order 3D Print'.
The menu item 'Available 3D Prints..." opens up the main ProteinScope 3D printed molecule store, where existing 3D prints of proteins in various styles and color schemes can be ordered right now.
Recent 3D print orders that have been made from this application device show the ordering URLs below the menu seperator, so you can get back to them between application sessions.
Use 'Clear Recents' if this list is getting unwieldy - BUT MAKE SURE you have bookmarked elsewhere the URLs you wish to return to at a later stage.



ProteinScope for Mac enables uploading of 3D prints of selected proteins to Shapeways.com for full color printing and order delivery.

Powered by Shapeways. The term "Shapeways" is a trademark of Shapeways, Inc. This application uses the Shapeways API but is not endorsed or certified by Shapeways, Inc.

To begin the 3D print ordering process, click "Order 3D Print" on the main toolbar to begin the printing dialog session.



ProteinScope 3D prints come with 3 base options - no base, a base with the PDIB ID printed on it, or a base with a QR code link printed on it:



If you have an iPhone or Android device with a recent OS version installed, hold the camera up to the image below and it will open the rcsb.org URL contained in the QR code.
In tests with 3D prints the QR code is a bit tricky to log due to the density of the codes, this will be addressed in future versions.
Proteins are printed to a scale of 1 Angstrom = 1mm, so the prints end up being about the size of a Keurig® K-Cup® Pod



After the base choice is made, click next and the model dimensions will be calculated and displayed.



The Shapeways material Sandstone is currently the only material available to ProteinScope for printing in full color. Three sandstone finishes are available:

Natural: This finish has a slightly rough surface and matte colors
Glossy: A glossy finish that provides good UV and moisture resistance ( + $5 )
Matte: A smoother finish that provides good UV and moisture resistance ( + $5 )

The colors used in the 3D printed model are the same as selected for displaying on screen.



You can choose to display the final 3D printed model on the main ProteinScope 3d prints storefront page for other users to order as well.
A private ordering URL can be selected also. While this is a non-public listing, the order will be known to the ProteinScope Shapeways account holder.
Any information entered upon ordering is subject the Shapeways privacy policy.
It is the responsibility of the user to keep a local copy of the private ordering URL.



All ordering URLs are stored application locally and will remain accessible from the "3D Printing" top level menu until cleared. Selecting the menu item will open the URL in the default browers.
Use the clipboard icon to copy the URL to the clipboard for pasting into other applications. Clicking the sharing icon will make the URL available to the standard sharing options.
Clicking on the order name text in the dialog will open the ordering URL in the default browser.



When the ordering page first opens, it will be mostly blank. Currently there is no notification if a model is not printable, just the preview will never render out. Only a small subset of proteins are 3d printable with the extant technique within ProteinScope, but this algorithm will be improved and the percentage of proteins that can be printed will increase.
Custom ordering is available for proteins that cannot yet be printed wth the automated methods.



Hit refresh on the ordering URL approximately every 5 minutes. If the model is printable, a rendered preview of how the model will look is displayed, along with the price of the model.
You do not need a Shapeways account to complete the order, guest checkout is available once you have added the product to the shopping cart by clicking the 'Buy Now' button.



To get a snapshot of the current protein view, click "Create Image" on the main toolbar. Select the location and name of the image file in the Save As dialog, then click "Save" to generate the snapshot image to the specified path location.



To get create a video of the protein rotation, click "Create Video" on the main toolbar. Select the location and name of the image file in the Save As dialog, then click "Save" to render the video of a rotation to the specified path location.



From the Help menu, clicking "ProteinScope Support" will open this page in the default browser.



The search bar can be used to locate a particular menu item.



Submit support or feature request

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