A protein data bank file is a database for 3D molecular files of nucleic acids, proteins, and other large molecules. These molecular files can store molecular structure. Some files of PDB might instead be in the protein data bank format, which is basically plain text files that store ensembles regarding protein structures. Some other files might be generated in the palmDOC or database file format and used with the mobile operating system of PalmOS. Now, if you are searching for how to open such files, then this blog will help you. Here you will see a complete guide on how to view PDB files on windows 10 and 11.
What Is A Protein Data Bank File?
Protein data bank files are a 3D molecular file format that annotates and describes protein and nucleic acid structure, such as atomic coordinates and secondary structure assignments. In addition, the PDB format is also a legacy file format for the protein data bank, which now holds data on biological macromolecules in the mmCIF file format. The file format is mainly used in bioinformatics to exchange protein coordinates. It consists of thousands of lines expressing a protein structure. Now, if you wish to view and open PDF files on a PC, you should use a devoted third-party tool, as there is no endemic application.
How to View Protein Data Bank Files in Windows 11?
There are only two ways to view a protein data bank file on your windows 10 and 11, including:
Method 1: Use Free Software to View PDB Files:
You can use third-party software for Windows PC that allows you to open and view PDB files. There are various free desktop applications available for Windows devices that you can try. Here are some top ones that you can easily use:
- iQmol
- Swiss-PDB viewer
- Cuomo
- Molecule
- RasMol
- iQmol
iQmol is a free, open-source visualization software and molecular editor for Windows 11/10. With this, you can view PDB files as well as other 3d files, e.g., MOL, SMI, CUBE, XYZ, etc. apart from that; you can also find all the essential molecule visualization tools. These tools range from basic to advanced ones. With iQmol, you can not only view PDB files, but you can also edit the molecular structure and open various files at the same time to view them all at once. From the panel of the model view, you can enable or disable the visualization of PDB files.
Top Features of iQmol:
- You can find standard file viewing tools such as pan, rotate, reset view, show axes, full screen, etc.
- It allows you to customize the model’s display by editing settings such as ambient, diffuse, fog strength, highlights, shoulder, noise intensity, POV-ray options, etc.
- You can add atom labels like partial charge, atom mass, NMR, spin density, etc.
- It lets you set up camera settings as per your affinity. You can modify the camera position and projection.
- It also offers an auto rotation feature that enables you to let the molecule rotate automatically.
- You can save the recent view of protein structure in a format of images like PPM, PNG, BMP, PS, JPG, EPS, etc.
- With iQmol, you can convert PDB files to other molecule files by using the save function.
- You can also use the “calculation feature” to compute PES scan, forces, molecular structure energy, geometry, energy decompose, BSSE correction, etc.
- swiss-pdbViewer
The Swiss-PDB viewer is a dedicated free PDB file viewer for windows 11/10 that lets you analyze and visualize various protein structures at the same time. With this, you can quickly analyze DNA structure also contained in a PDB file. Besides the protein data bank files, it allows you to open and view MMCIF and MOL files.
When you open the PDB file, you will see a 3D view of the interface with a control panel window. The control panel has some standard information, including the file header and list. You can also move the structure, zoom in, and rotate it. The Swiss-PDB viewer also lets you show or hide backbone, surface, H-bonds, and forces vectors, as per your choice. In addition, you get a lot of molecular modeling features such as computer energy, analyze domain, detect domain, generate 3D motif, build crystallography symmetry, and more tools also exist in it.
- CueMol
Cuomo is another free PDB viewer for windows 11/10. It is a visualization tool that is used to view PDB files. It lets you toggle between orthographic view mode or perspective and rotate or zoom in/out the model. You can quickly render the model using POV-Ray and animation rendering methods. It also offers a measurement tool that allows you to measure the model’s angle, distance, and torsion. With this, you can also find some extra tools to further analyze the structure of the protein. These tools include MOL surface cutter, molecular superposition, MOL surface generation, MOL bond editor, MOL morphing animation, etc.
- Molekel
The next software for PDB viewer is Molekel, an old but most powerful molecule software of visualizations. With this, you can find various molecule analysis and visualization tools to analyze protein structure. It also lets you customize the presentation of atoms, bonds, molecules, residues, etc. It can also customize 3D view properties, use shaders, show/hide bounding boxes, etc. it offers an animation feature used to play an animation of the molecule structure. An analysis menu with some respective tools is also present in it. Using the analysis tools, you can determine spin density, grid data, molecular electrostatic potential, distance, angle, and more of a structure.
- RasMol
To view a PDB file, you can use RasMol on Windows 11/10. Like other software, it also allows you to analyze and visualize molecular structures. With this, you can view the PDB structure in the wireframe, backbone, stick, strands, and ribbons form. It allows you to show and hide Hetero atoms, shadows, labels, Hydrogen, etc. in addition; you can measure torsion, angle, distance, and other values in a structure.
Method 2: Try A Free Online Tool To Read PDB Files
Now, You can use a free online tool to open and view PDB files. To start reading, you have to open the official website in your trusted web browser and upload your PDB file to view it. Here are a few free online tools for PDB viewers that you can try:
- RCSB PDB
- Molsoft
- RCSB PDB
You can use this RCSB PDB free online tool to visualize PDB files. This tool lets you import a protein data bank file, and then you can also visualize and analyze its molecular structure. With this, you will find basic visualization functions like rotate, zoom, toggle, reset the camera, expanded port view, toggle selection mode, etc., which offer an animation function. By using this, you can automatically spin the protein structure. While doing this, you are able to customize angle and rotation speed. Additionally, you will also get a measurement tool. With this, you can find out various values like orientation, angle, distance, and more.
- Molsoft
Molsoft is another free online tool that you can use to visualize. It is an elementary view of a PDB file that comes with basic features. To start with, you need to go through its official website and click on the menu option. Then, select the open option to start importing a saved file or uploading a file from your google drive. As you choose the file, it will show you the molecular structure. You can also use unique view modes such as wireframe, ball & stick, ribbon, CPK, etc. As per your demand, you can also toggle between these view modes. Molsoft also offers a measurement tool that you can use to measure the planar angle, distance, and torsion angle in the model.
Conclusion:
Protein data bank files are 3D molecular files that can be viewed using an online tool or software application. You can also try freeware such as IQmol, swiss-pdbViewer, and CueMol to analyze and visualize PDB structures on your Windows PC. If you prefer online tools, there are various options, like RCSB PDB and Molsoft. They both are free online PDB file viewers that offer analysis and visualization tools of molecules. This derailed blog will provide complete information about all the tools and software to view PDB files.
