What is Protein Data Bank (PDB) file?
Protein Data Bank (PDB) is a database for 3D structural data of proteins, nucleic acids, and other large molecules. A file with pdb file extension is basically a file containing data related to a 3D biological molecule’s structure. The data include atomic coordinates, atomic structures, atomic connectivity, protein structure, nucleic acid structure, and more. It also contains experimental metadata. This file format is largely used in Bioinformatics to exchange protein coordinates. It contains thousands of lines describing a protein structure. Now, if you want to read or view PDB files on Windows PC, you need to use a dedicated third-party tool as there is no native application to do so. In this post, we will be discussing different methods to view a PDB file in Windows 11/10.
How to view a Protein Data Bank (PDB) file in Windows 11?
There are two methods to view a Protein Data Bank (PDB) file on your Windows 11/10 that are as follows:
1] Use free software to view PDB files
You can use a third-party software for Windows that lets you open and view PDB files. There are multiple free desktop applications available for Windows that you can try. Here are some good ones that you can use:
IQmolSwiss-PdbViewerCueMolMolekelRasMol
A] IQmol
IQmol is a free open-source molecular editor and visualization software for Windows 11/10. Using it, you can view PDB as well as various other 3D molecule files, e.g., MOL, SMI, CUBE, XYZ, etc. You can find all the important molecule visualization tools in this software. These tools range from basic to advanced ones. Apart from viewing a PDB file, you can also edit the molecular structure. It lets you open multiple PDB files at once and view them all at once. From the Model View panel, you can enable or disable the visualization of one or more PDB files. Main Features of IQmol: The features of this free and open source PDB file viewer that you can look out for are:
You can find all the standard file viewing tools that include zoom in/ out (using the mouse wheel), pan, rotate, fullscreen view, reset view, show axes, etc.It lets you customize the model’s appearance by editing settings like shader, ambient, diffuse, fog strength, highlights, noise intensity, POV-Ray options, etc.You can also add atom labels like atom mass, partial charge, NMR, spin density, etc.It allows you can set up camera settings as per your liking. You can customize camera projection, position, etc.There is a handy Auto Rotation feature in it that enables you to let the molecular model rotate automatically.You can save the current view of protein structure in an image format like PNG, PPM, BMP, JPG, PS, EPS, etc.It also lets you convert PDB to other molecule files using the Save as function. The supported output formats are XYZ, MOL, MOL2, CML, etc.You can also use its Calculation features to compute molecular structure energy, forces, PES scan, transition state, chemical shifts, geometry, energy decompose, BSSE correction, etc.
Besides viewing features, you get a dedicated Build menu with a set of molecule building features. These features include adding new atoms, inserting new a molecule, minimizing the structure, setting isotopes, and many more. It is a really good molecular modeling software using which you can visualize Protein Data Bank files on your PC. If you liked it, download it from here. See: Chem4Word is a Chemistry Add-in for Microsoft Word. B] Swiss-PdbViewer
Swiss-PdbViewer is a dedicated free PDB file viewer for Windows 11/10. It lets you visualize and analyze multiple protein structures at a time. You can analyze protein structure, DNA structure, etc., contained in a PDB file. Besides the PDB file, it also lets you open and view MOL and MMCIF files. When you open a PDB file, the 3D view is shown on the interface along with a Control Panel window. The Control Panel contains general information, the list, and the header of the file. You can easily move the structure, rotate it, zoom in/ out, etc. It also lets you show or hide dot surface, backbone, H-bonds, forces vectors, and more as per your preference. You can also highlight different parts in distinct color schemes to analyze the structure better. Apart from that, you can use display features like Render in Solid 3D, Render POV, Display Labels, and some more. Apart from visualization tools, you also get a lot of molecular modeling features in it. Additionally, compute energy, compute H-bond, analyze domain, detect domain, generate 3D motif, build crystallography symmetry, and more tools are also present in it. You can download it from its official website. Read: Best free Nutrition Analysis software for Windows 11/10. C] CueMol
CueMol is yet another free PDB viewer for Windows 11/10. It is a macromolecular structure visualization tool using which you can view PDB files. Other files that you can open and view in it are DX, MAP, MTZ, CNS, etc. It lets you toggle between Perspective or Orthographic view mode, rotate the model, zoom in/ out, etc. You can render the model using POV-Ray and animation rendering methods in it. The rendered structure can be saved in PNG format. A measurement tool is also available that allows you to measure distance, angle, and torsion in the model. You can also find some additional tools to further analyze the protein structure. These tools include Molecular Superposition, Mol surface cutter, Mol surface generation, Mol bond editor, Interaction Analysis, Mol morphing animation, etc. It is a good software to visualize and analyze protein structure present in PDB files. See: What is a LIT file? How to convert LIT to EPUB or MOBI in Windows? D] Molekel
The next PDB viewer software on this list is Molekel. It is quite an old yet powerful molecule visualization software that lets you open and view PDB files. You can find a lot of molecule visualization and analysis tools that allow you to analyze protein structures. It lets you customize the display of molecules, atoms, bonds, residues, etc. You can choose different display types for each such as Ball & Stick, CPK, Hemisphere, SoSphere, Full Sphere, Cylinder, SoCylinder, Semicylinder, Wire, Stick, Line Ribbon, etc. Plus, you can customize 3D view properties, show/ hide bounding boxes, use shaders, etc. It lets you view the PDB file by changing the electron density of the structure surface and adding the solvent-accessible surface to the structure. You can find an Animation feature in it to play an animation of the molecule structure. A dedicated Analysis menu with respective tools is also present in it. Using the analysis tools, you can determine grid data, spin density, molecular electrostatic potential, radiation spectrum, distance, angle, and more of a structure. It also lets you convert your PDB files to various file formats. These formats include PDF, PS, EPS, and Image. If you liked it, you can get it here. Read: Complete Anatomy App is a worthy download for Windows. E] RasMol
You can also use RasMol to view PDB files on Windows 11/10. It is free and open-source software that allows you to visualize and analyze molecular structures. It also supports other files to open and view, such as MOL, XYZ, CIF, MOPAC, etc. It lets you view the structure in the form of Wireframe, Backbone, Sticks, Ribbons, Strands, etc. You can also highlight different parts of a structure in different colors. It also allows you to show or hide Hydrogen Atoms, Hetero Atoms, Shadows, Labels, etc., as per your preferences. You can also measure distance, torsion, angle, and other values in a structure. This software is available here. See: Best free 3D Human Anatomy software for Windows.
2] Try a free online tool to read PDB files
You can also use a free online tool to open and view PDB files. All you have to do is open the website in a web browser and upload your PDB file to view it. Here are some nice online free PDB viewers that you can try:
RCSB PDBMolsoft
A] RCSB PDB
You can use this free online tool called RCSB PDB to visualize Protein Data Bank files. It lets you import a PDB file and then visualize and analyze its molecular structure. You can find some basic visualization functions such as Zoom, Rotate, Toggle Expanded Portview, Reset Camera, Toggle Selection Mode, etc. It also lets you configure some settings or control options like camera mode (perspective or orthographic), background color, enable/ disable occlusion, enable/ disable fog, clipping, layout, etc. It comes with an Animate function. Using this, you can automatically spin the protein structure. While doing so, you can customize rotation speed and angle. You also get a dedicated Measurement tool in it. Using this tool, you can find out several values like distance, orientation, angle, and more. In addition to these features, some more handy tools available in it are Structure Motif Search, Add Components, Export Animations, Export Geometry (STL, OBJ, etc.), and Export Model. All in all, it is a really good free online PDB viewer with a great set of visualization tools. You can try it here. B] Molsoft
Molsoft is another online tool that you can use to visualize PDB structures. It is a simple PDB file viewer with basic features. To start with, open its website and click on the three-bar menu option. After that, select the Open option to import a locally saved PDB file or upload a file from your Google Drive. As you select the file, it will show you the molecular structure in its viewer. You can use different view modes to visualize the structure. These modes include wireframe, Creatine phosphokinase (CPK), ball & stick, ribbon, etc. You can easily toggle between these view modes as per your requirement. Besides that, it lets you enable or disable atom labels, residue labels, hydrogen bonds, and sites for a better understanding of the structure. It also provides measurement tools. You can measure distance, planar angle, and torsion angle in the model. Also, a handy Color by feature to color the structure by atom type, chain, alignment, secondary structure, and more is available in it. It is another good online PDB file viewer that you can try for free.
How do I download a PDB file from Protein Data Bank?
To download a PDB file from Protein Data Bank, you can visit the Protein Data Bank website and type and search with the name of the protein or Macromolecule like Human Hemoglobin, Chitinase, etc. After that, from the search results, select the file and use the download option to download the PDB file. As simple as that.
How do I view PDB structures?
The PDB molecular structures can be viewed using a dedicated online tool or software application. You can try freeware like IQmol, Swiss-PdbViewer, and CueMol to visualize and analyze PDB structures on your PC. If you prefer using an online tool, there are many options. For example, try web services like RCSB PDB and Molsoft. These are free online PDB file viewers that provide advanced molecule visualization and analysis tools.
How do I convert a PDB file to PDF?
To convert a PDB file to a PDF, you can use this free desktop application called Molekel. It provides a dedicated Save to PDF option that allows you to convert a PDB file to PDF format. You can open a PDB file and then click on the File > Save to PDF option to convert PDB to PDF. We have discussed this software in detail in this post, check out above. That’s it. Now read: Best free Molecular Modeling software for Windows.
