Molecular structure visualization tools

They derive in part from physical ball and stick models called Corey-Pauling-Kolton or CPK models that pre-dated computer visualization.

Those early colors for chemical elements see examples above were incorporated into early Molecular Visualization Software such as Kinemages , RasMol , and Chime. The CPK colors for chemical elements, and the DRuMS color schemes were incorporated into the color schemes built into Jmol , the visualization engine used in Proteopedia. See Help:Color Keys for color-key templates in Proteopedia.

Views tab of FirstGlance in Jmol. Features can be most easily displayed in the Views tab of FirstGlance in Jmol. Evolutionary conservation can sometimes be seen with one click in Proteopedia , or in other cases requires submitting a job to the ConSurf server. For a specific protein, such features can be displayed by using Proteopedia's Scene Authoring Tools and then attached to green links when authoring a page. Tools tab of FirstGlance in Jmol. FirstGlance in Jmol provides "one-click" routines, in its Tools tab, to highlight.

You can browse for molecular models at the Atlas of Macromolecules , the Molecule of the Month , or Protein Spotlight. Such atomic coordinate files can be formatted in a number of different file types chemical MIME types. Information about chemical MIME types can be found at:. The files of Dr. This chemical MIME type is often used for large molecules, especially proteins.

To view the structures that are encoded by these atomic coordinate files which have the extension. Here, we first describe a few 'Swiss Army knives' geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known.

Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives. PubChem is another one of simple molecule viewer software for Windows. It lets you browse molecule files and then visualize molecule structure in 3D. As you open a file, it displays molecules in both tiled and overlay structures. So, you can view single molecule structure or multiple molecules in tiles.

To view molecule, you can use options like rotate, scale, zoom, align, etc. Also, you can customize display options like atoms, bonds, molecules, box, symbol, etc. Using the Preference button, you can configure options like image quality, light model, background color, viewing angle, scale strategy, orthogonal projection, atom scale, atom coloring, atom info, bond coloring, bond info, bond width, etc.

VMD is yet another 3D molecule viewer for Windows. It provides separate windows in order to import and manage molecule files and for molecule visualization.

As you do that, it displays file information and 3D molecule view in dedicated windows. You can open multiple molecule files and toggle between each of them to view respective molecules. Like other molecular visualization software, it also lets you customize molecular view by configuring representation, color, materials, and labels. For better molecule viewing experience, you can use options like automatic rotation, perspective or orthogonal view, FPS indicator, change background, stereo, stage, render mode, etc.

Furthermore, you can configure your mouse in rotation, translate or scale mode, add atom, bond, angle, or dihedral labels, add or remove bonds, etc. Here are some of its features which ensure a nice molecular visualization experience:. It also supports loading Python scripts and extra plugins and lets you calculate secondary structure, H-bonds, and FDPB electrostatics.

UGENE is a free open source bioinformatics software which can be used as a molecule viewer for Windows. It supports a lot of file formats to import and analyze nucleic acid and protein sequences. You can customize various display settings which include rendering style, color schemes, molecular surface rendering style, set background color, etc. To know more about its key features, check this link. It is quite a basic molecule viewer as compared to other software in this list. It provides basic view options which include window size, disc smoothness, background color, atom properties, bond options, and label properties.

If you wish, you can save the molecular display as a PNG image. Along with molecule structure representation, it displays a Residue List too.