General Commands load [format]. Load a molecule pdb. Brookhaven Protein Databank others see documentation zap. Delete molecule exit. When RasMol starts, a second window is also opened where you can type commands to control the program. However, when this openis it is immediately. It includes RasMol commands that are especially important in the For more detailed information regarding all RasMol commands, consult the RasMol.
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Please type the RasMol commands 'help copying', 'help general', 'help IUCR', If you use RasMol V or an earlier version, type the RasMol command 'help. The original RasMol manual was created by Roger Sayle. RasMol can read a prepared list of commands from a 'script' file (or via inter-. Mouse Buttons. Clicking on an atom identifies that atom in the command window. Moving the mouse whilst holding mouse buttons and/or control keys.
Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling CPK spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces. The program reads in molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes.
If connectivity information is not contained in the file this is calculated automatically. The loaded molecule can be shown as wireframe bonds, cylinder 'Dreiding' stick bonds, alpha-carbon trace, space-filling CPK spheres, macromolecular ribbons either smooth shaded solid ribbons or parallel strands , hydrogen bonding and dot surface representations. Atoms may also be labelled with arbitrary text strings.
Alternate conformers and multiple NMR models may be specially coloured and identified in atom labels. Different parts of the molecule may be represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. The displayed molecule may be rotated, translated, zoomed and z-clipped slabbed interactively using either the mouse, the scroll bars, the command line or an attached dial box.
RasMol can read a prepared list of commands from a 'script' file or via inter-process communication to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image. The RasMol help facility can be accessed by typing "help " or "help " from the command line. A complete list of RasMol commands may be displayed by typing "help commands".
Mottarella et al.
Page 2 interface was implemented in and does not take full advantage of today's graphics processing units. Nevertheless, it is still widely used on computers running Windows, Linux, or Macintosh operating systems.
Its graphics are much more advanced and have become the standard in today's captured images. However, its scripting language is based on object- oriented Python and can be difficult for someone unfamiliar with computer science to learn.
It is also a complex language with many more commands than RasMol's simple language. The process involves searching for recognized, valid, RasMol script commands and performing their PyMOL equivalents, either as single commands or as a series of commands that produce the same result.
As we considered which commands to translate, it became clear that a number of features in PyMOL should be added to RasMol to make the two programs more complementary.
When a single command could be directly translated, we used simple code to recognize that command and perform its equivalent.
For RasMol commands containing multiple parameters, the command was translated into a series of PyMOL commands, which were executed sequentially. Several commands required altering PyMOL's default settings to produce exactly the same results. Moreover, several commands remain untranslated for various reasons including lack of universal features to mimic a RasMol code in PyMOL, and intentionally untranslated commands that would only serve to confuse users, such as help, where returning the PyMOL help would be of no use to a ConSCRIPT user.
This opens a dialog box that will enable the user to search for the script file.
Biochem Mol Biol Educ. Implementation The image of porcine pancreatic elastase in Fig.
The protein is shown in a cartoon representation with the catalytic triad and a bound inhibitor highlighted as wireframes. The script used to produce Fig. Then, the same RasMol script was used to reproduce the image from Fig. Also, the operation of the zoom command was different in scale and implementation linear in RasMol vs.
Our solution to this is quite simple. PyMOL does not recall the last selection automatically, even though it may remember it.
Commonly Used RasMol Commands
ConSCRIPT simply ensures that any command executed is executed on the previous selection by having a variable dedicated to the previous selection and forcing the PyMOL command to act on that selection.
The largest difference is in the script format—RasMol uses natural language scripting, whereas PyMOL uses object-oriented code. Finally, there were some RasMol commands including bond, connect, star, and strands that did not have equivalents in PyMOL and could not be implemented at the level of a plug-in.
The plug-in is available for download as a compressed file in both. Information on creating publication quality figures using PyMOL commands is included in the readme.
Page 4 Acknowledgments The authors thank the invaluable assistance of Frances C. References 1. Lesk, AM.
Schwede, T. Westin, C.These commands display a different prompt and are discussed in the command reference.
It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions. Also, the operation of the zoom command was different in scale and implementation linear in RasMol vs. Measuring angles A bond angle is determined by the relative positions of three atoms. Moreover, several commands remain untranslated for various reasons including lack of universal features to mimic a RasMol code in PyMOL, and intentionally untranslated commands that would only serve to confuse users, such as help, where returning the PyMOL help would be of no use to a ConSCRIPT user.
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