13 Best Free PDB Viewer Software For Windows

Here is a list of best free PDB viewer software for Windows. PDB or Protein Data Bank files carry textual data about three-dimensional structures of large biological molecules. It also carries information about atomic structures, atomic coordinates, protein structure, nucleic acid structure, etc. In order to view the 3D structure using the textual data from a PDB file, you need a PDB viewer software. These listed software quickly generate and show you the 3D molecular structure using a PDB file, which you can also analyze. To properly view a 3D molecular structure, these software offer some useful viewing tools like zoom, orientation, wireframe view, orthographic view, etc. Apart from PDB files, you can also open other molecular data containing files through these software such as ALC, BIO, CAR, MOL, HIN, etc.

In some software, you can also find useful editing and model enhancing tools through which you can add new nodes, redesign protein structure, change colors of structure modules, etc. Besides this, structural analysis tools like compute energy, compute H-bond, analyze domain, etc., are also present in these free PDB viewers. Rendering is another feature which is present in some PDB viewers which lets you render the molecular structure according to user-defined parameters. After rendering a model, you can save it in PNG, BMP, and other image formats. The textual data of a model can also be saved in formats like PDB, ENT, BIO, etc. In general, all of these viewers offer all necessary PDB file viewing tools plus some additional tools which you can easily use. Go through the list to know more about these software.

My Favorite PDB Viewer Software For Windows:

IQmol is my favorite PDB viewer software as it provides all essential 3D molecular structure visualization tools. Plus, it offers a lot of building tools which you can use to create new or to edit existing PDB file molecular structure.

Molekel is another handy PDB viewer software as it also offers essential visualization, analysis, and building tools.

You can also check out lists of best free Molecule Viewer, Molecular Modeling, and Molecular Mass Calculator software for Windows.

IQmol

IQmol is a free open source PDB viewer software for Windows, Linux, and MacOS. Using this software, you can visualize a PDB file molecular structure, edit molecular structure, build a new molecular structure, and perform molecular calculations.

Visualization of a molecular structure is quite easy in it as it immediately shows the molecular structure on its interface as soon as you load a PDB file to it. Plus, it lets you view model from all directions with the help of your mouse and allows you to zoom-in on the structure by using the mouse wheel. In it, you can also visualize molecular structure present in other file formats such as MOL, SMI, CUBE, etc. After visualizing a molecular structure, you can save it in the same PDB file or in other files formats like CML, MOL, GZMAT, XYZ, etc.

Key Features Of IQmol:

• Display: Using it, you can change the projection of the molecular model, adjust model appearance, and add atomic labels (atom mass, partial charge, spin density, etc.) to the model.
• Build: It provides various tools using which you can make various changes to the existing model like change in model symmetry, change in the force field, addition of new atoms, change in structure, etc.
• Calculation: Using it, you can calculate molecular structure energy, forces, PES scan, transition state, chemical shifts, etc.

Additional Features:

• Snapshot: It lets you take snapshots of the molecular structure in a particular view that you can save in PNG, PPM, BMP, and FIG formats.
• Animation: This feature takes continuous snapshots of the structure that you can save in BMP, PNG, and PPM formats.

Final Thoughts:

It is a really good PDB viewer software as it not only lets you visualize the molecular structure, but it also lets you perform other handy tasks like calculation, structure editing, structure building, etc.

Molekel

Molekel is another free open source PDB viewer software for Windows, Linux, and MacOS. Through this software, you can easily visualize 3D molecular structures of different molecular files including PDB like RXN, SDF, TMOL, VMOL, ZMAT, etc. The molecular structure provided by this software is very clean and easy to analyze. By clicking and dragging the mouse over the molecular structure, you can view the structure from different directions.

Main Features of this PDB File Viewer:

• Display: It lets you make changes on the 3D structure and also shows you all the changes to the structure in real time. Changes like Atom structure (Hemisphere, SoSphere, Full Sphere, etc.), Bond Structure (Cylinder, SoCylinder, Semicylinder, etc.), Residue structure (Wire, Stick, Line Ribbon, etc.), etc., can be made using it.
• Analysis: Using it, you can analyze grid data, spin density, molecular electrostatic potential, radiation spectrum, etc., of the molecular structure.
• Surfaces: It lets you change the electron density of the structure surface and lets you add solvent accessible surface over the structure.
• Animation: It allows you to record movements of the molecular structure in the form of animation.

After visualizing the 3D molecular structure, you can easily save it in PNG and TIFF image formats.

Final Thoughts:

It is another powerful PDB viewer software that offers all essential 3D molecular structure visualization tools.

Swiss-PdbViewer

Swiss-PdbViewer is a free PDB viewer software for Windows and MacOS. Using this viewer, you can view protein structure, DNA structure, and other information present in a PDB file. As soon as you open a PDB file in it, you can view a 3D molecular model created by this software using the PDB file data. To view the model from all directions, you can click over the model and drag your mouse. In this software, you also get a lot of analysis tools to analyze PDB model to know more about the molecular structure. After visualization and analysis of the 3D molecular structure, you can save it in the same PDB and in POV and PNG formats.

Features Of Swiss-PdbViewer:

• Display: It provides all the necessary PDB model viewing tool such as rotate, axis, show dot surface, show backbone, show H-bonds, etc.
• Build: Using it, you can edit the existing PDB model design by adding bonds, residues, c-terminal, and other components. Plus, options to remove residue, bond, and break backbone are also present in it.
• Tools: It is a menu that offers various model analysis and computational tools like compute energy, compute H-bond, analyze domain, generate 3D motif, and more.
• Color: It allows you to highlight different parts (force field, sidechain, proteins, etc.) of the model in different colors.

Final Thoughts:

It is simple and easy to use software if you just want to view PDB file data in the form of a molecular structure.

Zeus

Zeus is another free PDB viewer software for Windows. It is primarily a molecular visualization software in which you can also view molecular structure of XYZ, MOL, SYBYL, and some other formats. Through this software, you can easily generate a molecular structure by loading a PDB file containing the molecular structure data. Along with the molecular model, it also shows Atoms table (it contains atoms ID, Name, and Coordinate information), Bonds table (it shows atoms bond, type, length, and description), and Structure table (it contains Phi, Psi, Omega, and Chain information.). In it, you can also find some really good viewing and computational tools.

Main Features:

• View: It provides all essential molecular structure visualization tools such as View Model, View Atoms, View Structures, View Bonds, Wire Frame, Auto Rotate, etc.
• Tools: It offers some 3D Structure editing and computing tools like Compute H-Bonds, Compute and Add Hydrogens, Bond non-bonded atoms, Clear H-Bonds, etc.

Additional Features:

• Find Sequence: Using it, you can find any particular molecular sequence of the model by typing the initial sequence.
• Color: It lets you view the molecular structure in Monochrome or in Retro Computing color (Green color).

Final Thoughts:

It is another good software to generate and view a molecular structure using a PDB file.

Molegro Molecular Viewer

Molegro Molecular Viewer is yet another free PDB viewer software for Windows. With the help of this software, you can quickly generate a molecular structure using PDB file data. Apart from PDB, you can also use this software to view MOL, MDL, SDF, and ENT files. It is helpful to just view and analyze the generated molecular structure.

To generate and view a model, you just need to load a PDB file to this software. For closely analyzing the structure, you can use the mouse wheel as it lets you zoom in on the structure. Plus, by hovering the cursor over the molecular structure, you can view properties of different structural bonds like bond length, number of atoms, dihedral angles, etc. After viewing and analyzing a PDB molecular structure, you can export it in PDB, MOL, and ENT file formats.

Features of Molegro Molecular Viewer:

• View: It lets you view the structure in different modes like Docking View, Preparation View, Electrostatic Interactions, Pose Organizer View, etc.
• Tools: Using it, you can analyze different aspects of a model like Surfaces, RMSD Matrix, Protein Hydrogen Bonds, Structural Protein Alignment, etc.
• Rendering: It allows you to render the structure in the form of wireframe, stick, ball and stick, or space fill.

Final Thoughts:

It is another really good PDB viewer software to properly view and analyze different aspects of the generated PDB structure.

Biodesigner

Biodesigner is a free molecular modeling and visualization program that can also be used as a PDB viewer software. In this software, you can also view molecular models present in files of other formats like ENT, ALC, BIO, CAR, MOL, HIN, etc. Not only this software lets you view molecular models, but it also offers various computing tools to calculate important aspects of a model. In it, you can also get some building tools to make enhancements to the existing molecular model. After viewing and enhancing a model, you can save the model in PDB, ENT, and BIO formats.

Main Features:

• View: It allows you to view the structure, structure atom number, atom name, residuum name, bond angle, torsional angle, distance between RMS deviation, and more structure parameters.
• Build: Using it, you can rebuild bonds, verify protein chain, renumber atoms, and create a mirror image of the 3D structure.
• Compute: Through this feature, you can calculate structural alignment, RMSD distance, RMSD coordinates, and other parameters of the structure.

Additional Features:

• Style: It lets you change the look of the structure by letting you manually define atom color, atom material, backbone style, backbone color, etc.
• Rendering: It allows you to add or remove antialiasing, motion blur, shading, depth cueing, and other effects from the 3D protein structure.

Final Thoughts:

This PDB viewer offers all essential viewing tools along with some handy enhancement tools.

CueMol

CueMol is yet another free PDB viewer software for Windows, MacOS, and iOS. It is primarily a macromolecular structure visualization tool that also allows you to view the molecular structure present in files like PDB, DX, MAP, MTZ, CNS, etc. The good thing about this software is that it even lets you view multiple molecular structures at a time because of its multitab interface. In this software, you get some handy molecular structure enhancement and rendering tools using which you can also create publication-ready molecular structure images.

Features of CueMol:

• View: Using it, you can view the 3D molecular structure of the PDB file in either Perspective or Orthographic view.
• Render: It allows you to render the molecular model using POV-Ray and animation rendering methods. Before rendering the structure, you can also define various rendering parameters like DPI, Resolution, Size, Projection Type, etc. After rendering the model, you can view as well as export the rendered structure in PNG image format.
• Tools: It offers some molecular structure editing tools like mol surface cutter, mol surface generation, mol bond editor, etc.

Final Thoughts:

This PDB viewer comes with some powerful molecular structure rendering and editing tools which you can use to further enhance the model.

PubChem

PubChem is the next free PDB viewer software for Windows and MacOS. It is a simple molecular structure visualization software in which you can view molecular structure present in a PDB file. Apart from PDB, it can also be used to view molecular data of PC3D, ASN, SDF, GZIP, and XYZ files. As soon as you open a PDB file in it, this software shows its molecular structure in two separate viewers namely Overlay and Tile. According to your requirements, you can also make changes to the structure using atoms and bonds settings.

Main Features:

• Overlay Viewer: This viewer shows the graphical 3D molecular structure that allows you to closely analyze each bond and atoms of the structure. After viewing the molecular structure in this viewer, you can save it in PNG and JPG image formats.
• Tile Viewer: In it, you can view a lot of different formations of the input PDB file molecular structure for better understanding of the structure.
• Atoms: You can access it from the options menu that gives you options to scale atom size, change atoms color, make atoms invisible, hide carbons, etc.
• Bonds: It provides options through which you can change bonds color, enable bonds info, make bonds invisible, adjust bonds width, etc.

Final Thoughts:

It is a simple yet powerful PDB viewer in which you can view 3D molecular structure of a PDB file.

RasMol

RasMol is one more free open source PDB viewer software for Windows. It is a simple 3D molecular structure visualization software that offers some great visualization tools. However, this software does not offer any analysis tool. In it, you can simply load PDB, MOL, XYZ, CIF, MOPAC, and other files and view their protein molecular structure. Apart from viewing the structure, you can also make modifications on the default structure through this software. After visualizing and making adjustments to the structure, you can save it in BMP, GIF, PPM, PICT, VRML, and other file formats.

Features of RasMol:

• Display: It allows you to visualize the 3D structure in modes like Wireframe, Backbone, Sticks, Ribbons, Strands, etc.
• Colors: It lets you highlight different parts of the molecular structure in different colors like groups, molecular chain, etc.
• Options: Using it, you can enable or disable Hydrogen Atoms, Hetero Atoms, Shadows, Labels, etc., of the molecular structure.

Limitations:

Lack of Zoom feature is the main limitation of this software as it restricts you from closely analyzing the molecular structure.

Final Thoughts:

It is a simple and straightforward PDB viewer software through which you can quickly visualize a 3D molecular structure.

QuteMol

QuteMol is yet another free open source PDB viewer software for Windows and MacOS. It is a dedicated molecular viewing tool that generates a high-quality visualization of 3D molecular structure using PDB and VDB files. As soon as you load a PDB or VDB file to this software, you can view a 3D molecular structure on its interface. Not only, you can view a 3D molecular structure in it, but you can also make various changes on the colors and structure of the default 3D molecular structure.

Features of QuteMol:

• Presets: This software comes with various presets using which you can change the look, colors, and shades of the default 3D molecular structure. Presets like Realistic 1, Cool, Simulated (S.E.M.), Shape Perception, etc., are present in it.
• Geometry: It lets you change the default geometry of your structure to Space-Fill Geometry, Licorice Geometry, and Balls n Sticks Geometry. Plus, options to change atoms and chains colors are also present in it.
• Customize: It lets you manually adjust lighting, light intensity, base color, depth cueing, halos, and other parameters of the 3D structure to customize its looks.
• Snapshot: After making all the adjustments to the molecular structure, you can use this feature to take snapshots of the structure which you can save in PNG, JPG, and GIF formats.

Final Thoughts:

It is another straightforward PDB viewer software that allows you to visualize and adjust PDB molecular structure.

VMD

VMD is the next free open source PDB viewer software for Windows, MacOS, and Linux. It is one more molecular visualization program that lets you visualize 3D molecular structures using data of PDB, OFF, MOL, PLY, PQR, GRASP, and other files. In this software, you can also open multiple PDB files to view multiple 3D molecular structures.

Along with a 3D molecular structure, this software also shows all important properties of the structure like number of atoms, number of bonds, number of residues, number of fragments, etc. Like many other PDB viewer software, this one also lets you customize the molecular structure according to your requirements. After making adjustments to the molecular structure, you can save its data in VMD file format.

Main Features of VMD:

• Display: Using it, you can adjust the molecular Model View (Perspective or Orthographic), Depth Cueing, Lighting, Background Color, Axes, etc.
• Graphics: Through this feature, you can adjust the look and feel of a molecular structure by manually specifying the Color Profile, Material, and Labels.
• Analysis: Using it, you can perform analysis on Hydrogen Bond, Salt Bridges, NAMD Energy, NAMD Plot, and more elements of the structure.

Additional Feature:

• Rendering: It lets you simply render the structure and save it in BMP image format.

Final Thoughts:

It is a free and feature-rich PDB viewer software that offers tools through which you can easily analyze and visualize a 3D molecular structure of a PDB file.

BALLview

BALLview is a free molecular modeling and visualization tool that can also be used as a PDB file viewer. This software is available for Windows and MacOS platforms. Apart from PDB, it also supports other molecular file formats namely MOL, SD, AC, and XYZ.

Features of BALLview:

• Display: Using it, you can adjust the camera angle to view the 3D molecular structure from different angles. Plus, general orientation tools like rotate, move, picking, etc., are also available in it.
• Build: In it, you get many molecular structure building tools which you can also use to make changes on the existing molecular structure like Build Bonds, Build Peptide, Generate Crystal, Add Hydrogens, Set Element, etc.
• Molecular Mechanics: Using it, you can simulate molecular dynamics and perform single point calculation on input PDB molecular structure.
• Export: After visualizing and modifying the input molecular structure, you can use this feature to export the molecular structure in PNG, STL, VRML, POV, and some other formats.

Final Thoughts:

It is a feature rich and powerful PDB viewer software that offers some really good visualization and 3D structure building tools.

COSMOview

COSMOview is another one of free PDB viewer software for Windows. Using this software, you can generate and view 3D molecular structure using data present in PDB, SDF, COORD, WRL, CCF, and other file formats. Just by loading a PDB file in it, you can view its 3D molecular structure. By using your mouse and mouse wheel, you can easily move around the 3D structure and also zoom at any part of the structure. After viewing the structure, you can save it in the PNG format.

Features:

• Toggle Wireframe Display: Using it, you can view the molecular structure in wireframe view.
• Viewer Options: Through this option, you can manually define structure bond line width, radius, bond colors, atoms radius, background color, etc.

Limitations:

Some features of this software are not working such as Toggle Sigma Surface, Toggle Molecule, Display Info, etc.

Final Thoughts:

It is one of the simplest PDB viewer software through which you can quickly view a PDB molecular structure. However, it does not provide any analysis tool like other similar software.