Oakland, California – Independent developer, Mark S. Morris is today announcing the release of ProteinScope(R) for Mac. Previously released for Windows in 2002, ProteinScope has been used in online encyclopedias, research paper publications, and was recommended in the U.S. Federal Registry by the Patent and Trademark Office for use in drug patent applications.
ProteinScope(R) for Mac enables full color 3D printing of eligible proteins, using structure files from the RCSB Protein Data Bank. ProteinScope for Mac is hand-optimized for use with the very latest features in macOS Mojave 10.14, providing a fast, smooth user interface and rendering of molecules. ProteinScope can have multiple protein windows open simultaneously, and can display individual proteins in full screen mode.
ProteinScope connects to the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) to retrieve structure information. ProteinScope is not endorsed in any way by the RCSB or any other institution. ProteinScope for Mac parses the major elements of the PDB XML (PDBML) file to display the molecule. 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. The proteins being displayed will auto rotate. Use the mouse wheel (or equivalent) to zoom in and out.
PDB XML can also be downloaded directly 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 accessible via the ProteinScope File menu item ‘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.
Proteins can be displayed in different styles; Space-fill and Carbon Backbone. Atom coordinates are interpreted as 1 Angstrom = 1 SceneKit Unit. For Space-fill, 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 – designed to allow the display of secondary, tertiary and quaternary structures of molecules
* Temperature – Red is hotter, blue colder. Not all PDBs have this information
* Hydrophobicity – Blue is more hydrophilic, red more hydrophobic
The 3D printing features of ProteinScope can accessed from the “3D Printing” top level menu. With a protein open, menu item ‘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. Recent 3D print orders that have been made from this application device show the ordering URLs below the menu separator, so you can get back to them between application sessions.
If you have an iPhone or Android device with a recent OS version installed, holding the camera up to the QR code 3D printed on the base of the protein will open the rcsb.org URL contained in the QR code. Proteins are printed to a scale of 1 Angstrom = 1mm, so most prints end up being similar in size to a C or D battery. Protein 3D prints are created with full color sandstone printing. Three sandstone finishes are available: natural, glossy and matte. The colors used in the 3D printed model are the same as selected for displaying on screen.
* macOS 10.14 or later
* 4.3 MB
Pricing and Availability:
ProteinScope is Free and available worldwide on the Mac App Store in the Reference category.
The Protein Data Bank: rcsb.org. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. Nucleic Acids Research, 28: 235-242. (2000)
SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules. Stephen V.Evans, Journal of Molecular Graphics Volume 11, Issue 2, June 1993, Pages 134-138
Mark S. Morris is an independent software and 3D printing developer in Oakland, California. ProteinScope is part of the uplink.to network. ProteinScope is (R) and (C) Mark S. Morris 2019. All Rights Reserved. Apple, Mac and macOS are trademarks of Apple Inc., registered in the U.S. and other countries. Other trademarks and registered trademarks are the property of their respective owners.
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