How do I use RasMol?

To open a file: File/Open from within RasMol. From within Netscape, click on a RasMol viewable molecule (a . pdb file). (RasMol should automatically start and load in the molecule.)

What is RasMol and its commands?

RasMol allows the execution of interactive commands typed at the “RasMol>” prompt in the command-line window (a window separate from the graphics window). Each command must be given on a separate line. Keywords are case insensitive and may be entered in either upper or lower case letters.

How does RasMol measure distance?

There are two ways to measure distances between atoms in version 2.6beta of RasMol. The first is to use the “set picking distance” command, to set the mouse into interactive distance measurement mode. Then by clicking on pairs of atoms, RasMol will report the distance between them on the command line.

How do I change the background in RasMol?

The background color of the display may be changed from the default (black) to a chosen color by typing background color at the Rasmol> prompt in the command line window. For example, Rasmol> background white changes the background color to white.

What is RasMol used for?

RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank.

What is RASWin?

RASWin (Risk Assessment Software for Windows) is a subscription-based software tool to develop and maintain machine functional safety documentation. It helps you manage your progression through the safety lifecycle.

What is a PDB path?

Program database (PDB) is a proprietary file format (developed by Microsoft) for storing debugging information about a program (or, commonly, program modules such as a DLL or EXE). PDB files commonly have a . pdb extension. A PDB file is typically created from source files during compilation.

What does Ramachandran plot tell you?

The Ramachandran plot is a plot of the torsional angles – phi (φ)and psi (ψ) – of the residues (amino acids) contained in a peptide. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.

What determines secondary structure?

The secondary structure of proteins is determined by the pattern of hydrogen bonding. A large number of server and tools are used to predict the secondary structure analysis.

What is PyMOL used for?

PyMOL, a cross-platform molecular graphics tool, has been widely used for three-dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories. It is also capable of editing molecules, ray tracing, and making movies.

What are pdb symbols?

pdb) files, also called symbol files, map identifiers and statements in your project’s source code to corresponding identifiers and instructions in compiled apps. These mapping files link the debugger to your source code, which enables debugging.

How do debug symbols work?

Debug symbols typically include not only the name of a function or global variable, but also the name of the source code file in which the symbol occurs, as well as the line number at which it is defined. All of this additional information can take up quite a bit of space, especially the filenames and line numbers.

How do I open RasMol in command line?

To open the Command Line Window, click on the RasMol Command Line button on the task bar. Arrange the Molecule Visualization window and the Command Line window so that you can see both windows and they are not overlapping. You can resize the windows to accommodate your preferences or computer monitor size.

What are the features of the RasMol program?

RasMol Features. RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh,…

Which is the input file format for RasMol?

Supported input file formats include Protein Data Bank (PDB), Tripos Associates’ Alchemy and Sybyl Mol2 formats, Molecular Design Limited’s (MDL) Mol file format, Minnesota Supercomputer Center’s (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files.

Why is RasMol quick start not complete by itself?

You will of course need to know how to use your web browser, and how to download files with your web browser. The main purpose of RasMol Quick Startis to guide you through the large number of pages at the RasMol Classic Main Page. Therefore, RasMol Quick Startis not complete by itself.