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.It was originally developed by Roger Sayle in the early 1990s. The main purpose of RasMol Quick Start is to guide you through the large number of pages at the RasMol Classic Main Page. Therefore, RasMol Quick Start is not complete by itself. As you go through it, you will be directed to other sections of the RasMol Classic Main Page by hyperlinks (usually colored blue and underlined). You will have to read.
- Introduction
- Setup of RasMol and Netscape
- Instructions for RasMol
WHAT IS RASMOL?
Available for Windows, Macintosh, and UNIX platforms, RasMol is a free, interactive molecular-graphics viewer. The program reads in the 3-D coordinates for a molecule using the pdb file format. It displays the molecule in various representations and allows one to rotate the molecule interactively. RasMol-ucb allows simultaneous viewing of multiple molecules.
HOW TO OBTAIN RASMOL AND TO SETUP NETSCAPE TO USE IT.
Rasmol Pdb
- To Download RasMol V2.6 ucb:
The version of RasMol that we are using (RasMol-ucb) is the enhanced version developed by Marco Molinaro from the UC Regents/ModularCHEM Consortium. How to download chess on mac. Be aware that this program is still in beta testing; thus, you may encounter bugs. It is based on the original RasMol that was developed by Roger Sayle at Glaxo, UK. (Reference: Roger A. Sayle and E. J. Milner-White, 'RasMol: Biomolecular graphics for all', Trends in Biochemical Science (TIBS), September 1995, Vol. 20, No. 9, p.374.)
- Download the PC Windows version of RasMol-ucb. To install the PC windows version, double click on the Rasmol2.exe installer program. It is a self-extracting program and the executable is RasWin. This version runs under Windows 3.1, Windows 95, and Windows NT.
- Download the MAC version of RasMol-ucb. To install the MAC version*, double-click on the Rasmol-mac.sea program. It is a BinHex’ed, self-extracting archive for the Mac and PowerMac.
*NOTE TO MAC USERS: To download RasMol correctly from the internet, you need to have either 'Stuffit' or 'Binhex' on your Macintosh. These are free software programs and are available on the ACN (Academic Computing Network) Macintosh network or from Aladdin Systems. Download chrome 80 for mac. Font download mac os x. If you have any questions about this, please see R. Frey.
- To set up Netscape to use RasMol-ucb:
- If using Netscape 4.0, go to Edit/Preferences. (If using an older version of Netscape, go to Options/General Preferences/Helpers (or Helper Applications).) A dialog box will appear.
- Create New Type of Navigator Application for RasMol: In category section on the dialog box’s left side, use the mouse to click on the word 'Application' under the category 'Navigator.' Use the mouse to click the 'New' button. Enter the following information in the text fields that appear (NOTE: The text fields MAY or MAY NOT be in this order!).
- Descripter: chemical/x-pdb
- MIME type: chemical/x-pdb
- Suffix (Mac) or File Extensions (PC): pdb
- Action: launch application: RasMac (RasWin) (Use 'Browse' or 'Choose' button to find RasMac/RasWin on your hard drive. When RasMac/RasWin is highlighted, press <enter> or click the 'Open' button. MAC Users: You will have to use the mouse to select the radio button named 'Application.'
- Click 'Ok' or press <return> to return to Netscape Navigator.
INSTRUCTIONS TO USE RASMOL:
- Basic Instructions (using the menus):
- 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.)
- To open multiple files (i.e., can view up to 5 molecules simultaneously): File/Open (for each file, without closing the previous files) from within RasMol. From within Netscape, just click on another RasMol viewable molecule.
- To select a molecule: Click on molecule name in the Molecules window (the secondary window)
- To close a file (a molecule): File/Close when the molecule is selected.
- Moving the molecule(s):
- <alt><SHIFT>and right-mouse button
- To change to different representations (i.e., CPK, stick, ribbon, etc.): Display/Stick
- To determine distances, angles, dihedral angles:
- Click on appropriate icon in the Molecules window (the secondary window)
- Click once on the appropriate number of individual atoms. (With angles, clicking on atoms must be in the appropriate order.)
- To rotate bond (Note: This changes the angle.):
- Click on rotate angle icon in the Molecules window (the secondary window)
- Click on 2 atoms
- Click on rotate angle icon in the Molecules window (the secondary window) again
- Click on 3rd atom
- Use mouse button to rotate
- To color molecule in different ways:
- To color by the protein-secondary structure: Colours/Structure
- a -helices: magenta
- b -sheets: yellow
- turns: pale blue
- all other residues: white
- To color by residue type (i.e., each type of residue is colored a specific color): Colours/Shapely
- To color by atom type (below are the default colors): Colours/CPK
- Carbon: gray
- Hydrogen: white
- Oxygen: red
- Nitrogen: blue
- Sulfur: yellow
- Iron: yellow
Action
PC
MAC
Rotation
Left-mouse
button (Click & Hold)Mouse button (Click & Hold)
Translation
Right-mouse
button (Click & Hold)https://intensivetek541.weebly.com/copy-os-to-new-drive-mac.html. <OpenApple> and
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left-mouse button<SHIFT> and
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<option><SHIFT> and
mouse button - Advanced RasMol Usage:
The command line may also be used to perform more advanced commands. To find the commands, look in the RasMol manual under Help (PC) or ð/Basic Instructions. Other helps, such as reference manuals and tutorials, are available on the Internet:
- http://www.curtin.edu.au/curtin/dept/biomed/teach/biochem/tutorials/GetStart.html
- http://macweb.acs.usm.maine.edu/chemistry/GR/GraphicsGallery/RasTut.html
- http://klaatu.oit.umass.edu/microbio/rasmol/distrib/rasman.htm
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Hp officejet 7612 driver download mac. Revised July 29, 1999