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What is ModView and how to use it
ModView is a free software tool that allows you to visualize and analyze multiple biomolecule structures and/or sequence alignments. It can interface with local or remote bioresources to provide graphical user interface (GUI) and analytical tools. ModView is used as a database interface in several structure-sequence protein resources[^1^] [^2^].
In this article, we will show you how to download, install and use ModView to explore biomolecular data.
How to download and install ModView
To download ModView, you can visit the official website of the developer, Valentin ILYIN, at https://modview.software.informer.com/. There you can find the latest version of the software, which is 0.903 as of March 2023[^1^] [^2^]. The download size is 399 KB and it is compatible with Windows operating systems.
To install ModView, you just need to run the downloaded executable file (MODView.exe) and follow the instructions on the screen. The installation process is simple and fast, and it does not require any additional software or libraries.
How to use ModView
Once you have installed ModView, you can launch it from the Start menu or the desktop shortcut. The main window of ModView consists of four panels: the menu bar, the toolbar, the structure panel and the sequence panel.
The menu bar provides access to various options and settings of ModView, such as file operations, view modes, analysis tools, help and documentation.
The toolbar contains buttons for common tasks, such as opening files, zooming in and out, rotating and translating structures, selecting atoms and residues, coloring schemes, displaying labels and annotations, etc.
The structure panel displays the 3D representation of the biomolecule structures that you have loaded or downloaded from bioresources. You can manipulate the structures using the mouse or the keyboard shortcuts. You can also change the rendering style, lighting effects, background color and other visual parameters.
The sequence panel shows the sequence alignment of the biomolecules that you have loaded or downloaded from bioresources. You can scroll through the alignment using the mouse wheel or the arrow keys. You can also edit the alignment, add gaps, insert or delete sequences, etc.
To load a biomolecule structure or a sequence alignment from your local files, you can use the File menu or the Open button on the toolbar. You can choose from various file formats, such as PDB, FASTA, CLUSTALW, etc.
To download a biomolecule structure or a sequence alignment from remote bioresources, you can use the BioResources menu or the Download button on the toolbar. You can choose from various databases, such as PDB, UniProtKB/Swiss-Prot, SCOPe, CATH, etc.
Once you have loaded or downloaded your data, you can use ModView to perform various analyses and comparisons. For example, you can:
Calculate distances, angles and dihedrals between atoms or residues
Measure surface area and volume of structures
Identify secondary structure elements and domains
Align structures based on sequence or structure similarity
Superimpose structures using rigid-body or flexible methods
Calculate root-mean-square deviation (RMSD) and structural similarity index (SSI)
Perform cluster analysis and principal component analysis (PCA)
Generate Ramachandran plots and other graphical representations
To access these analysis tools, you can use the Analysis menu or the corresponding buttons on the toolbar. You can also customize the parameters and options of each tool according to your needs.
ModView is a powerful and user-friendly software tool that enables you to visualize and analyze multiple biomolecule structures and/or sequence alignments. It can interface with local or remote bioresources to provide GUI and analytical tools. ModView is used as a database interface in several structure-sequence protein resources.
If you are interested in exploring biomolecular data using ModView, you can download it for free from ec8f644aee