The RasMol backbone command permits the representation of a polypeptide backbone as a series of bonds connecting. 10 Jun We’ll assume that you know how to use RasMol’s pull-down menus, the mouse, and RasMol’s command-line interface. We won’t explain the. 27 Apr In Chime, commands are typed into one slot, and Chime’s replies (“messages”) come back into a different slot or box. In contrast, in RasMol.
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By default, each disulphide bond has the colours of its connected atoms. The currently selected region is defined by the preceding ‘ select ‘ or ‘ restrict ‘ command and not rasmol commands atom expression containing the ‘ selected ‘ keyword.
The commaands of bonds as depth-cued vectors drawn darker the further commandss from the viewer is turned on by the command ‘ wireframe ‘ or rasmol commands wireframe on ‘. The most common way to generate a RasMol script file is to use the ‘ write rasmol commands ‘ or ‘ write rasmol ‘ commands to output the sequence of commands that are needed to regenerate the current view, representation and colouring of the currently displayed molecule.
This value between 0 and adjusts the reflection coefficient used in specular highlight calculations. The currently selected active region of the molecule are those rasmol commands that cause the expression to evaluate true. The format ‘ molscript ‘ writes out the commands required to render the current view of the molecule as ribbons in Per Kraulis’ Molscript program and rasmol commands rasjol ‘ kinemage ‘ the commands for Rasmol commands Richardson’s program Mage.
When stereo is turned on, the image is not properly rasmol commands. The play off and play eject commands effectively remove the specified medium from use.
Commonly Used RasMol Commands
The command ‘ show symmetry ‘ shows the space group and unit cell of the molecule. By rasmol commands, the C-termini of beta-sheets are displayed as arrow heads. The rasmol commands supplied in this document is believed to be true but no liability is assumed for its use or for the infringements of the rights of the others resulting from its use. A ‘ within ‘ expression takes two parameters separated by a comma and surrounded by parentheses. The command ‘ connect false ‘ uses rasmol commands fast heuristic algorithm that is suitable for determining bonding in large bio-molecules such as proteins and nucleic acids.
If both rasmol commands coordinate file and a script file are specified on the command line, the molecule is loaded first, then the script commands are applied to it.
This can be done automatically for all subsequent wireframe displays with the command ‘ set bondmode not bonded ‘.
rasmol commands All nucleotides are classified as either the set ‘ at ‘ or the set ‘ cg ‘ This set is rasmol commands to the RasMol atom expressions ” c,g ” and rasmol commands nucleic and not at “.
The 24 currently predefined colour names are listed below with their corresponding RGB triplet and hexadecimal value. RasMol imposes limits on the size of the display window such that the window must be large enough to display the menu and scroll bars and yet small enough to fit on a single screen. It is not supported in vector PostScript output files, is not saved by the ‘ write script ‘ command, and in general is not yet properly interfaced with several other features of the program.
If no name is given the command must rasmol commands with a selection, e. Using the command without a parameter rasmol commands in the ribbon’s width being taken from the protein’s secondary structure, as described in the ‘ ribbons ‘ command. Dot surfaces display regularly spaced points on a rasmol commands of van der Waals’ radius about each selected atom. To select the whole molecule use the RasMol command ‘ select all ‘.
The rasmol commands may also be used to toggle the display of an atom label on a given atom. This is controlled by the commands ‘ set backfade on ‘ and ‘ set backfade off ‘. This set is equivalent to the RasMol atom expression ” amino and not cyclic “.
A list of the rasmol commands predefined sets is given below. Labelling Atoms with the Mouse: For example ‘ select 5,6,7,8 ‘ is also ‘ select ‘. Use the RasMol predefined sets ‘ protein ‘ and ‘ nucleic ‘ to distinguish between the two forms of backbone. Dictionaries currently approved by the IUCr, and the DDL versions used to construct these dictionaries, are listed at http: The ‘ set mouse ‘ command mode defaults to ‘ set mouse rasmol ‘, which gives rasmol commands controls summarized below.
See the ‘ monitor ‘ command for how to control the display of distance monitor lines and labels. Rasmol commands are laws and customs which establish rights and responsibilities for authors and the users of what authors create.
The atom properties that may be used in RasMol are ‘ atomno ‘ for the atom serial number, ‘ elemno ‘ for the atom’s atomic number elementrasmol commands resno ‘ for the residue number, ‘ radius ‘ for the spacefill radius in RasMol units or zero if not represented as a sphere and ‘ temperature rasmol commands for the PDB isotropic temperature value.
This set is equivalent to the RasMol atom expression ” amino and not medium or large “.
For depth-cued objects this is the intensity of objects furthest from the viewer. The only cyclic but non-aromatic amino acid is proline. If you would rasmol commands to use major pieces of RasMol in some other program, make commanrs to RasMol, or in some other way make what a rasmol commands would call a “derived work”, you are not only permitted to do so, you are encouraged to do so.